Are there any differences between the GECKs? Like do I need both to work on both games or can I just use 1 GECK? Kinda annoying if I should need to download both as I still play fallout 3.
Would rather have 1 GECK downloaded and running then 2.
Yes, they are different and produce different version .esps. The FNV GECK also has numerous issues documented extensively in other topics. You'll just have to bite the bullet and keep both on hand. There was a recent thread that had an .ini setting that's needed to run them at the same time, if that'll help you at all, I'd look for it.
I was wondering the same thing and came across http://www.gamesas.com/index.php?/topic/1140021-about-geck/ if you want to run both the FO3 and FONV GECKs at the same time