Old thread, but this is what i did.
Once the usb is setup and all files have copied move the scraper files to the retropie-mount folder on the USB.
mv ~/.emulationstation/downloaded_images /media/usb/retropie-mount/
mv ~/.emulationstation/gamelists /media/usb/retropie-mount/
Since retropie automounts the items in the retropie-mount dir into the ~/RetroPie/ dir we can create symlinks to point the that ~/RetroPie/ and no need to change the sources in the files.
ln -s ~/RetroPie/downloaded_images/ ~/.emulationstation/downloaded_images
ln -s ~/RetroPie/gamelists/ ~/.emulationstation/gamelists