My mods aren't showing in game, even though they are installed.

I just got finished manually installing mods in me3tweaks mod manager, and when I boot up the game the mods don't show up at all.
I've opened the game from me3tweaks and from steam (there was quite a bit of file validation so I don't know if that may have caused any problems) and I've triple checked to make sure that each mod was installed on the proper game. Any advice?