Server under linux gets installed in /usr/local/Repetier-Server/. Easiest solution is to make it a link to your usb directory.
All data entries are store under /var/lib/Repetier-Server/
whcih you can also make a link to your usb drive. Then you could just install it as normal and it would run from usb. Or you copy it somewhere else and adjust the config files telling server where the new directory is, but that might interfere with updates, so just using a link to usb and install is in any case easier.
