i'm gonna post the reply i got that ended up working for me:
Open "Archive.exe" in your steamapps/common/skyrim folder. It was installed with your Creation Kit.
It's a more advanced .bsa packer. Make sure the .bsa file you make in Archive.exe is spelled EXACTLY the same as your .esp
Then when you go to upload your mod, it will find the already made .bsa file
next time i started up creation kit, it said "Mod.bsa already found, use it?", I assume that's why the name needs to be the same. Hope that helps.