Whenever I launch my normal game through the FalloutNV launcher, only some of the mods I installed work like Nevada Skies and CASM but other ones like Ihud and mcm dont show up unless i launch NVSE, This started occruing after I tried to remove enhanced shader mod? Any help?

By my understanding, one *should always* launch NVSE...

(I assume you're talking about "Launch NVSE" through FOMM)

Thats what im talking about... lol i feel like an idiot now. As you have probably assumed by now I am new to modding, please forgive me .