[Murph]

If you are using the mods wrapper, you should only need to move each individual mod's folder into the main "MODS" folder in the game's main folder.
The only exception is maps- you need to have a folder called "MAPMODS" inside the MODS folder. Within that folder is another called simply "MAPS". New or modified maps go in there.
Most final release maps come with a self installer anyways, just point it to your MODS folder.