I'm very new to the fallout modding world, I own both games on Steam and have the Fallout NV version of the G.E.C.K.
I was wondering: Can I use this version to create Fallout 3 mods, or only mods for NV? I tried installing the none-NV version but whenever I try, it just wants to modify my nv version of G.E.C.K. I've worked a lot in the 3d animation and modeling field and am quite anxious to import my own creations, as well as getting into level design (something I haven't done since Half-life). Sorry if this is a very noob question...

The GECKs are not interchangable. You need to use the F3 one for F3 and NV for NV. Renaming the shortcuts can help avoid confusion. The FNV GECK can't properly load the F3 esm so it should be rather clear if you have the wrong editor/esm match.