Nexus mod manager doesn't install mods please help

[PCSharkey]

I have been trying to install mods on both fallout new vegas and skyrim and I am stilling running into this problem. I download and activate the mod on the NMM and it says that the mod was successfully installed for example project nevada, when I launch the game I use NVSE and when I get in game there is no sign of the mod but when I installed it through FOMM I was instantly greeted with a mod screen telling me the controls and I didn't get that using the mod manager. This happens with every mod despite it saying it was succesfully activated and the esp file being checked in the games settings. The only things that work with the mod manager are texture packs. Can anyone help me out thanks