Yeah, I know the program you're talking about, it's pretty neat and very useful. You should be able to simply place the .exe in the main game folder and run it, it should auto-create a sub-folder called 'MODS', in here you should place your mods in folders of their own, making sure that the structure of the folders for each mod is correct (mirrors actual game folder organization) so that when you run the program it copy-pastes everything to where it's meant to be. Then you should then be able to swap mods in and out nice and simply.