After a few failed attempts I finally got this all sorted out. For anyone interested I used the following command to get all my roms in /media/usb1/roms/nes/ to scrape as well as the sub-directories correctly without having to edit any other file.
pi@raspberrypi:~ $ /opt/retropie/supplementary/scraper/scraper -output_file="/home/pi/emulationstation/gamelists/nes/gamelist.xml" -missing="/home/pi/.emulationstation/gamelists/nes_missing.txt" -image_dir="/home/pi/.emulationstation/downloaded_images/nes" -image_path="/home/pi/.emulationstation/downloaded_images/nes" -rom_dir="/media/usb1/roms/nes" -rom_path="." -thumb_only -workers 4
the nes_missing.txt I though would be useful so that I can find which I need to manually edit.