I know I left aproximately ten in each walled city five indoors and five outdoors and the other cities similarly plentiful ammouts, a good ammount to get a collection going.

I left one in the Cizero Dawnstar Sanctuary (pre vamped) and one in the burning sanctuary Falkreath, so you can actually only get those two during a playthrough.

I found the Mud Skull in the Helgen keep in the room where you kill those two stormcloaks that were searching for supplies.

I've got all the ones for whiterun and riverwood that I can find for now. I restarted to make sure I got all I could find. Here they are so far:
Helgen
Helgen Keep- Blue eyes- Mud
Riverwood
Sleeping giant inn- Blue eyes- Dark Cloud
Hod and Gerdurs- Blue eyes- Dark Mourners
Whiterun:
Warmaidens- Blue- Unicorn Hunters
Bannered Mare- Blue- Argonia
Shrine of Talos- Blue- White rock
Dragons Reach (really need to look for this one)- Blue- White Storm
Hall of the Dead- Blue- Aftermath
House of clan Battle-Born- Blue- White Horse Hunter\
Amrens House- Blue- Ocean Floor
Jorrvaskr- Blue- Violet Storm
Outside Jorrvaskr on barrel in back- Red- Man Hunter Skull
Sky forge- Red- Small Isle
Outside Bannered Mare on Barrel- Red- Mannequin hunter Skull
Temple of Kynareth- Blue- Vamp Eye Skull
Outside Ysoldas House on Barrel- Red- Moon Eye Skull



Thats all for tonight. I may post more in the next day or two.

Top of the tower before Bleak Falls Barrow- Red- Gowned Skull
Bleak Falls Barrow (outside)- Red- Boot Strap Skull
Bleak Falls Sanctom- Blue- Sovenguard Skull
Anises Cabin- Red- Blue Storm Skull
Alchemists Shack- Red- Sovenguard Skull
Path to High Hrothgar (2nd emblem)- Red- Third Eye Skull
High Hrothgar (supply chest)- Red- Stone Skull
High Hrothgar (inside)- Blue- Mourners SKull
High Hrothgar (inside)- Blue- Pilgrim Skull
High Hrothgar (court yard)- Red- Straw Skull
Lost Valkygg- Green- Nordic, Mudd, Pilgrim, Painted, Merchant, Marsh, Moss, Miden, Priestess, Pale Doom, and Mason Skulls
Shalidor's Maze- Green- Kindel, Leatherbound, Leatherman, Lichen, Markarth Sack, Markarth Sheild, Markarth Tower
Ustengrav Depths- Blue- Veridian Skull

Shroud Hearth Barrow- Blue- Twain Doom Skull
Trevas Watch- Blue- Sea Stone Skull

Falkreath:
Outside Deadmans drink on barrel- Red- Lichen Skull
Deadmans drink-Blue- Packers Skull
Outside Dengeirs House- Red- Marsh and Markarth Shield Skull
Outside Corpse light farm- Red- Markarth Tower Skull
Inside Corpse light farm- Blue- Mothman Skull
Jarls Longhouse- Blue- Penitus Skull
Under Lod's workbench- Red- Markarth Sack skull
Grave Concoctions- Blue- Palomino Horse Hunter Skull

Bloated mans Grotto- Green- Red Eye, Orange eye, Shadow, Snowcat hunter, Stormcloak, and Summer set skulls

Solitude:
Winking Skeever- Blue- Arkay Skull
Radient Raiment- Blue- Bear Skull
Angelines Aromatics- Blue- Straw Skull
Bits and Pieces- Blue- Blue Skull
Catacombs- Blue- Brow Beaten Skull
Temple of the Divines- Blue- Torstens skull
Fletcher- Blue- Blood Red Skull
Thalmor Headquarters- Blue- Stone Skull
Bards College- Blue- Crystal skull
Blue Palace- Blue- Blue Glow Skull
Red Wave- Blue- Beard Skull

Statue of Meridia- Red- Huntsman Skull
Kilkreath Balcony- Red- Yellow Doom Skull
Kilkreath Catacombs- Blue- Woodland and Huntsman skull

Dragon Bridge:
Four Shields Tavern- Blue- Gowned SKull
Outside Four Shields Tavern- Red- Emparor Skull
Outside Penitus Oculatus Outpost- Red- Falkreath Shield Skull
Penitus Oculatus Outpost- Blue- Gowned Skull

Gjukar's Monument- Red- Black Horse Skull
Rorik's Manor- Blue- White Beard Skull
Abandoned Camp Before Chillwind Depths- Red- Mothman Skull
Sinking Ruins- Red- Torsten's skull key
Outside Deadman's Respite- Red- Brown Eye Skull
Inside Deadman's respite- Blue- Gowned Skull
Robbers Cove- Blue- White Rage Skull

Chillfurrow Farm by chopping block- Red- Gray Storm Skull
Battle Born Farm by Grindstone- Red- Fortress Skull
Inside Battle Born farm- Blue- Groom Skull
Broken Fang Cave- Blue- Thieve master skull

Riften:
Bee & Barb- Blue- Falkreath Shield Skull
Black-Briar Meadery- Blue- Emparor Skull
Temple Of Mara- Blue- Dawnstar Skull
Talos Shrine- Red- Torstens skull key
Honorhall Orphanage- Blue- Dragon King Skull
Romlyn Doeths House- Blue- Whiterun Skull
On top of barrel before temple of mara- Red- Argonia Skull
Aerins House- Blue- Dias Del Morte Skull
on barrel outside fishery- Red- Mage Guild skull
On barrel under stairs outside beggers row-Red- Aftermath skull
On Barrel outside beggers row- Red- Whitestorm SKull
The Ragged Flagon Cistern- Blue- Dawnstar Shield Skull
On Tombstone by Thieves Guild Entrace- Red- Arkay Skull

Shors stone
Filnjars house- Blue- Vampiric Skull

Dawnstar:
Windpeak inn- Blue- Gowned Skull
Dawnstar Barracks- Blue- Boot Strap Skull
The White Hall- Blue- Gowned Skull
By Smelter in cart- Red- Rogue Hunter Skull
Iron Breaker Mine- Blue- Deer Hunter Skull
The Mortar and Pestle- Blue- Fortress Skull
Outside Beitilds house- Red- Sabrecat Hunter Skull
OutsideLeigelfs House- Red- Road Skull
On SHip- Red- Red Guard Skull
Fruki's House- Blue- Charred Skull

Winterhold:
Outside Frozen Hearth- Green- Huntsman Skull
Inside The Frozen Hearth- Blue- Small Isle Skull
Jarls Long House-Blue- Man Hunter Skull
Outside Kraldar's House- Green- Yellow Skull
Inside Kraldars House- Blue- Black Sand Skull
Pathway Entrance to college- green- Yellow Doom
The Arcanaeum- Blue- Fire Rune, Fox Pelt Skull
Archmage Quarters- Blue- Snowfur Hunter Skull
Hall of Countenace- Blue- Moon Eye Skull
The Midden- Blue- Mannequin Hunter Skull
The Midden Dark- Blue- Forest Skull

Fellglow Keep- Blue- Pentius Skull

Labyrinthian Chasm- Green- Forest Skull
Labyrinthian Chasm- Green- Black Coast, Black Sand Skull
Labyrinthian Tribune- Red- Brow Beaten Skull
Labyrinthian Tribune- Red- Blue Glow, Blood Red Skull- Green- Fox Pelt, Gray Skull

Misty Grove- Blue- Beggers Skull

outside Wolfskull Cave- Green- Woodland Skull
Inside Wolfskull Cave- BEFORE you get The Man who Cried Wolf Quest- Blue- Black Coast Skull
Dustman's Crypt- Blue- Gray Storm Skull

Windhelm:
Stables- Blue- Gray Skull
Brandy Mug Farm- Blue- Tech Skull
Holly Frost Farm (in Chicken coop)- Red- Vampiric Skull
Docks Warehouse- Blue- Orrange Skull
The North Wind (Ship)- Red- Twain Doom Skull
Candlehearth Hall- Blue- Stormcloak Skull
Blacksmith Quarters- Blue- Vampire Eye Skull
The White Phial- Blue- Olive Eye Skull
Hall of the Dead- Blue- Snowcat Hunter Skull
House of clan Shatter Shield- Blue- Torsten Skull Key
House of clan Cruel Sea- Blue- Rising Doom Skull
New Gnisis Corner Club- Blue- Skeever Hunter Skull
Outside Sadris Used Wares- Red- Shadow Skull
By East Side City Exit Door- Red- Red Eye Skull
Palace of the Kings- Blue- Shadow Skull
Calixtos House of Curiosities- Blue- Summerset Skull
Hjerim- Blue- Leaf Skull (I pickpocketed key)

(I was having some odd glitches with the Wolf Skull Cave quest. Even when I was able to get the quest by going to the blue palace and sitting through the dialoge, the sinkhole wouldn't show up. I reloaded, and then the dialoge didn't trigger to get the quest. Typing in setstage MS06start 15 will make it to where you can just talk to Falk Firebeard without sitting through the dialoge and it will fix the sinkhole not showing up IF you are having problems with the quest like I was.)

Fort Hraggstad Prison- Blue- Afflicted Hunter Skull
Ironback Hideout- Red- Volcanic Skull
Dragontooth crater- Red- Favajey Skull
Haemars Shame- Blue- Nordic Skull
Rimerock Burrow- Blue- Whiterun Shield Skull
Adandoned Shack- Blue- Castle Skull
Outside Abandoned Shack- Red- Gravel Skull
The Ragged Flagon cistern- Blue-Dawnstar Shield Skull
Outside Bilegulch mine-red- Gowned Skull
Goldenrock Mine- Blue- Bluestorm Skull
Outside Goldenglow estate- Red- Veridian Skull
East Empire Company warehouse- Red- Crystal, Dark Cloud, Dark Mourners Skulls
Brinewater Grotto- Red- Dawnstar, Dark Brotherhood, Dias Del Morte Skulls
Abandoned Horse Camp (By Snow Veil Sanctum)- Red- Gowned Skull
Journeyman's Nook- Red- Winterhold shield and Woodland Skulls

Markarth
Inside Temple of Dibella- Blue- Markarth Shield Skull
Markarth Stable's- Blue- Marsh skull
Outside Salvius Farmhouse- Red- Rising Doom SKull
Inside Salvius Farmhouse- Blue- Volcanic Skull
Silver Blood Inn- Blue- Mason Skull
Arnlief and son'e- Blue- Moss Skull
Ogmund's House- Blue- Merchants Skull
On Pillar by Treasury House- Red- Violetstorm Skull
Outside abadoned House- Red- Unicorn hunter Skull
The Hags Cure- Blue- Miden Skull
Blacksmith Ghorza's- Red- Vampire Eye Skull
Understone Keep- Blue- Markarth sack and Lichen Skulls
Dwemer Museum- Blue- Leatherman Skull
Calcelmo's Tower- Blue- Kim and Kindel Skulls

Twilight Sepulcher- Blue- Scale Skull
Dainty Sload Deck- Red- Ravenmain and Robo Skull
Japhets Folly 9on the deck after battle before heading back to windhelm)- Green- Forest Dragon
Black Briar Lodge- Blue- Dock Skull
Hag Rock Redought Ruin- Blue- Painted Skull
Gallows Rock- Blue- Briarheart Hunter Skull
Driftshade Refuge- Blue- Graymain Skull
Yngvild Throne Room- Blue- Ragnar Skull
Ysgramor's Tomb (outside)- Red- Black Wolf Skull
Ysgramor's Tomb- Blue- Priestess Skull
Tolvalds cave- Blue- Setting Doom Skull
Forsaken Crypt- Blue- Robo Gray Skull
Craked Tusk Keep- Blue- Affronted Skull
Frostmere Crypt- Green- Dragon King, Emparor, and Falkreath Shield Skulls

Morthal
Morthal Jail- Blue- Grass Skull
Alva's House- Blue- Hard Rock and Green Stone Skulls
Falion's House- Blue- Green Skull
Highmoon Hall- Blue- Granit Skull
Thaumaturgist's House- Blue- Forest Dragon Skull
Thonnirs House- Blue- Rune Fire Skull
Mooreside Inn- Blue- Rune Frost Skull
Jorgen & Lami's House- Blue- Frost Skull

yngol Barrow- Blue- Black Beach Skull
Angis Camp- Red- Beggers and Aqua eye skulls
Drelas Cottage- Red- HjaalmarchSkull
On Table going up path to Eldersblood peak- Red- Hard Rock and Hrothgar Skulls
Giants Grove- Green- Blue- Blue, Blue Glow (2), Blood Red, and Brow Beaten Skull's
Fallowstone Cave- Green- Dias Del Morte, Dark Brotherhood, Dawnstar Shield, and Dark Mourners Skulls
Forelhost Crypt- Blue- Potema Banner Skull
Reachwind Eyrie- Blue- Windhelm Shield Skull
Karthspire- Green- Green Stone, Hard Rock, Hrothgar, Grass, and Granite Skulls
Sky Haven Temple- Blue- Third Eye Skull
Alfthand Cathedral- Green- Castle and Friend Skull
Black Reach- Green- Gravel, Ravenmain, Groom, Gowned, Sabercat Hunter, Afflicted Hunter, Rogue Hunter, Road, Ice Eye, Graymaiin, Graystorm, Grayman, Gowned, Penitus Grey, Stockade, Stagl, Sovernguard, Pine, Dock, Mothman, Argonian hunter, Briarheart Hunter, Argonian Skin Hunter, Robo Gray, Vermina, Aqua Eye, Thing, Vangeful, Beggers, Bluestorm, Boot Strap, Charred, Fortress, Potema Banner, and Pentius
Silent Ruins- Blue- Pine Skull

As for direct locations for the ones in black reach, sorry, you are on your own. I HATE black reach, I even may have missed some, I do not know for sure. I know I miss some in the cities now and again, but always add tehm if I find more. So, so far only found 35 in Black Reach. I will only go back and search again at the end of my game, when I have nothing else to do, becasue like I said, I really do hate that place. lol

Nightgate Inn- Blue- Falkreath Skull
Fort Dunstad (on top of prison tower)- Red- Moss Skull
Fort Dunstad Prison (lower levels)- Blue- Ravenmain Skull
Pinepeak Cavern- Blue- Mage Guild Skull
On path up to Autumnwatch Tower- Red- Frost Skull
Archwind Point- Red- Stockade (by grave), Stagl (top of farthest tower)
Northwind summit- Red- Granit and grass skulls
Northwind mine- Blue- Yellow doom skull
Outside Angarvunde- Red- Thieves master, thing skulls
Fort Greenwall (captain's quarters)-Blue- Rouge HUnter Skull
Fort Kastav (very top of tower)- Red- Ragnar, Pale Doom, and Priestess Skulls
Bonechill Passage- Blue- Stockade Skull
Fort Amol- Red- Merchant Skull
Lost tongue overlook- Red- Green, Green Rock, Green stone skulls
Morvunskar- Red- Tundra, toxic Skulls
Crovangr cave- Blue- Yellow Skull
Fort Fellhammer mines- Blue- Redguard skull
Glenmoril Coven- Blue- Brown Eye Skull
Silverdrift Lair- Blue- Tundra Skull
Outside darkshade- Red- Dragon King Skull
Broken limb camp- Red- Gray Man Skull (2)
Raldbthar- Blue- Winterhold Skull
Blizzard rest- red- Gowned SKull
Deepwood Redoubt- Red- Silver Eye and executioner skulls
Deepwood Vale- Green- Vampire eye, White Rock, Temple, Unicorn Hunter, Violet Storm, Vamp Eye, White Horse Hunter Skulls
Blind CLiff Cave- Green- Olive Eye, Snowfur Hunter
Red Eagles Ascent- Green- Rising Doom, Rough Emerald, Strassus, Ocean FLoor, Rune SHock SKulls
Soljunds Miners House- Blue- Stitchers Skull
Old Hroldan Inn- Blue- Winterhold SHield Skull
Broken Tower Redoubt- Blue- Thing Skull
Ruins with Dwemer Convector North of Markarth- Red- Ice Skull
Mor Khazgur Cellar- Blue- Hjaalmarch Shield Skull
Laraks Longhouse- Blue- Hjaalmarch Skull
Mor Khazgur Mine- Blue- Hrothgar Skull
Dushnikh Yal (alchemist shelves)- Red- Kim, Kindel, Leather Man Skulls
Burguks Longhouse- Blue- Gray Man Skull
Mauhulakhs Cellar- Blue- Bar Maid Skull
Mauhulakhs longhouse- Blue- Favajey Skull
On Barrel outside gloombound mine- Red- Forest Skull
On barrel by bed outside gloombound mine- Red- Fox Pelt Skull

On bridge right past Fort Amol- Red- Castle Skull
Fort Neugrad- Blue- Argonian Hunter Skull
Gloom Reach Cavern (in cart)- Blue- Executioners Skull
Lost Valley Redoubt- Red- Sea Stone, Scale, Setting Doom, Snow, Solitude Shield, Solitude Skulls
Cradle Stone Tower- Red- Deer Hunter SKull
Bannermist Tower- Red- Gowned Skull
Dragon Reach Porch- Gree- Windhelm Shield, Winterhold, Whiterun Shield, Whiterun, Mage Guild Skulls
Outside Gallows rock- Red- Strassus, Rune Shock Skulls
Fort Sungard- Red- Rough Emerald, Ocean Floor, Leaf Skulls
Fort Sungard Annex- Blue- Argonian Skin Hunter Skull

*Palace of the Kings- Blue- Red Eye Skull*

I was wondering, will your mods ever be available on the Nexus? Management of installs and Uninstalls is a little better for me using the nexus. I'd understand if it is a no. Enjoying your mods nonetheless. :)

@Annwyn, you are skull mistress ;)
@BubSwifey, I'm not publishing on the nexus ever again.