Technically, OBJ files can be saved anywhere as long as you know its location and have easy access.  If you follow Poser's folder hierarchy convention, the OBJ file should be placed within the Geometries folder in an easily accessible subfolder.  It could be the same folder as the original, as long as the original is not overwritten.  Once a conforming garment is created, it is advisable not to relocate the OBJ file elsewhere afterwards.  Doing so, will break the absolute path the conforming clothes needs to find the OBJ file.