@steptoe are you talking about the RetroPie-Manager?
If yes, be aware that the tool is made to manage ROMs only in the usual paths (which is ~/RetroPie/roms and ~/RetroPie/BIOS). If you want to make the tool point to the external USB drive my suggestion is to create symbolic links.
Maybe something like this:
ln -s path/to/roms/dir/on/your/usb/drive ~/RetroPie/roms
ln -s path/to/BIOS/dir/on/your/usb/drive ~/RetroPie/BIOS