You should be able to perform the update on the main battery. The backup battery will not charge until at least 12.25 volts is seen within the SV screen (install manual, page 9-4).
Ground power, in your case, is an external charger on the main battery. Many chargers cannot power everything on the main bus and still produce 12.25 volts. Shut down as many things as possible and allow the main battery to get to 12.25 or more and you should see the backup battery charging.
If it still doesn't work, plug directly into the back of the display. Failing that, get a different USB stick (each screen comes with one).