Yes, you can have as many folders as you want inside the custom folder.

Yeah that error is common and isn't one you should have to be worried about.

halflife2.fgd will throw errors in Hammers error reporter but you can ignore them. Are you sure it is causing hammer to crash?

An FGD file is basically a recipe book for entities, it tells hammer "this is entity is called this, has these keyvalues that can be set, and these are the inputs and outputs it has".

FGD doesn't determine assets, that's all taken care of by the gameinfo.txt for the game/mod.

You can open up an fgd file in a text editor like notepad++ and take a look at it if you want to see what entities it adds. The halflife2.fgd for example includes all the information for hl2 entities like npc_combine_s and npc_citizen. If you're not going to be using any HL2 entities then you don't need to use it and just using the CSS one should be fine.

The only reason I can think of that would crash hammer from an fgd is if there was for some reason an entity conflict between two fgds and even then it should just revert to mount order.

There is a limit to the number of textures you can have mounted if you are mounting to many it could be the cause of the crash.

Looking at HL2's vpks, hl2_misc is the only one of the vpks that actually contains models.

See if removing the TF2 ones fixes the issue with HL2 ep2 and the episodic content, I want to say TF2 has some content that name conflicts with HL2's.

Double check the gameinfo.txt located in Steam\steamapps\common\Source SDK Base 2013 Multiplayer\customConfig

Are you using multiple hard drives by any chance for steam and/or steam games?

That is one of the main new features in the next release which is a complete overhaul :)

http://steamcommunity.com/groups/SourceMultiTool/discussions/0/630800445536594133/

What config are you trying to use? Is it customConfig? If so you need to do an initial setup and select some of the .fgd's (it's what determines what entities you can place).