when I need to tell a world model to look to a different .nif, I open up the thing in FO3edit and put the path to the .nif to be exactly what I need. I don't know if it can be done in GECK, I have not seen a way.
I would. It's enabling. Personally, I don't use the archives so it's easier to tinker with stuff. You can always extract the archives and keep them handy just in case. I keep mine on an external and have all the .ini (GECK and game) bUseArchives lines set to 0 and have commented out the sArchiveList lines to keep my primary drive out of the red.