I just set retropie up as well, I am using a regular 8Gb SD Card to boot the system. Obviously, that is way too little to store all the systems I want, so I decided to use a spare 32Gb Pendrive i had lying around.
I found the most simple way to do this would be to simply let the folder “roms” point to my usb stick instead using a soft link. This has the advantage of the default es_systems.cfg being left untouched, when you update retropie using the setup script it’ll revert to the default cfg file, forcing you to manually edit your cfg again. but by soft linking /media/usb to ~/RetroPie/roms, the roms are now in the correct place for RetroPie to find them.
For me, I simply formated the pen drive to use the ext4 filesystem (Retropie would not load roms from the drive if it was formated as FAT32) using the command ‘sudo mkfs.ext4 /dev/sda’ and correcting the permisions afterwards (sudo chmod -R 777 /media/usb). I then moved the folder ~/RetroPie/roms to /media/usb (sudo mv ~/RetroPie/roms /media/usb) and created a soft link to the correct place (sudo ln -s /media/usb/roms ~/RetroPie) and tested a few games. Everything works just fine.
