When I plug my flash drive in, a window pops up and asks me if I want to open it up in File Manager, I do that and it opens right up.

I tried to do over my network, but my Pi does weird things trying to access my Samba share, but that’s not a RetroPie issue.

You should really get a 512 Model B if you really want to do serious emulating on the Pi, aside from the extra USB port, you also get double the RAM. I guess a model A would be good if all you wanted to do was some single player action, you could just hook a hub up just to load ROMs.

On a side note, the joyconfig utility is really just there to let you know what the physical buttons and axis translate to as far as the digital buttons are concerned, my suggestion is to go through joyconfig with each type of controller and notate what buttons and axis are defined there and configure them manually.