For those of you who wish to publish maps you created in hammer, but do not know how (like I, before I found out), it's quite simple. Locate your Portal 2 bin directory ("C:\Program Files (x86)\Steam\steamapps\common\portal 2\bin" for me) and search for an application called "p2map_publish". Opening this application will pop up a File Browser. From here you have several options to choose from.

PLEASE NOTE: As far as I know, it is not possible to "Edit" (and update) an item (map) you have already posted on the workshop from PTI (hopefully Valve will alow this at some point in the future). Thus any updates to your map (that you have created in Hammer) cannot overwrite your workshop item created within PTI. THEY ARE NOT CONSIDERED THE SAME WORKSHOP ITEM.

For example: You create "Test01" in PTI. You publish it to the workshop within PTI and it gains 10 views. You decide to edit and update it in Hammer. You open "p2map_publish" (no published maps in the File Browser shown). You attempt to add the same map with the same published name "Test01" to the workshop. You will get an error saying something about that name being already used. This is because the PTI item is created and stored seperately from the one you edited in Hammer. BE CAREFUL!

So if you wish to publish a custom map (created partially from PTI and Hammer), do not publish it in PTI beforehand (or instead publish them as "private")! Otherwise any views, favourites, etc. will be lost. The maps are located in the following folder: "C:\...\Steam\steamapps\common\portal 2\portal2\maps\workshop"

Edit: To clarify, they are not "lost" in the sense that they disappear. You simply lose the progress you had by adding a second workshop item with updated features to the first, assuming you want people to play the updated version.