I was trying to add a slightly altered texture/mesh/thing for a pistol to make sure I was doing it right, but it always says "Invalid Directory" whenever I try to edit the new pistol in G.E.C.K. Is there a specific folder I should keep the meshes and textures folders on? (after using FoMM to extract them)

Meshes for meshes, Textures for textures? You can make subdirectories e.g. Meshes\Toaster and Textures\Toaster.