You can mount the usb stick once and then either link or mount its directories. For this simple purpose, links and mounts should be mere preference, although they have some differences. I prefer mounts for their heightened transparency to the system, but others prefer links.
Just search the web for either "linux symlinks" or "linux bind mount" for a ton of how-tos about them, like this one or this one.
edit: If you put the contents of roms in the root directory of the stick, you can also mount it directly onto the roms dir on your memory card. Mind that this will make anything in the card's roms dir unavailable for the duration of the mount.