I believe I may have found a solution, at least according to Monorail Cat. If you don't need the solution don't waste your time reading this crap.
I got him to use the config for CSS, changing the game configurations to the ones I used for the old Gmod, so there probably will still be some unsolved problems which I don't know about later on.
I got him to change his engine version to "Source Engine MP" for CSS and then change a few directory locations and add the .fgd files from the "\sourcesdk\bin\orangebox\bin" folder along with the Gmod and ttt.fgd, which I trust most of you placed in your Gmod folder.
Because I'm too fucking lazy and I don't know what I'm even doing he changed his directories to the following:
Game Executable:$SteamUserDir\garrysmod
Game Directory:$SteamUserDir\garrysmod\garrysmod
Hammer VMF Directory:$SteamUserDir\garrysmod\garrysmod/maps
Then in the "Build Programs" tab
Game Executable:$SteamUserDir\garrysmod\hl2.exe
BSP Executable:$SteamUserDir\sourcesdk\bin\orangebox\bin\vbsp.exe
VIS Executable:$SteamUserDir\sourcesdk\bin\orangebox\bin\vvis.exe
RAD Executable:$SteamUserDir\sourcesdk\bin\orangebox\bin\vrad.exe
Place compiled maps:$SteamUserDir\garrysmod\garrysmod/maps
Someone please correct me if I'm wrong (which I should be). I have little experience with Hammer. At least this configuration should allow you to map normally, not too sure about compatibility with gamemodes and all that. Cheers.