do you have the IWAD from both games in that folder?
I recommend you do--- more stuff to load is always good.
anyways you should just start gmod normally, the stuff is under npcs, weapons and entities
you can play the entire games within gmod (sorta)
there is a tab on the tools and settings thing.
if you dont load the doom wad when playing let's say E1M1-Hangar you WILL get missing textures.
you cannot spawn the levels into any other map than gm_flatgrass.