We use the Blue Ox Patriot system also. We tow a 6 speed Mini behind our Sprinter based ERA (class B) MH. I set the controller on 5 as any higher setting locks the Mini tires when I apply the ERA brakes,
As far as the battery goes, I had the same issue with the battery being run down after a 2 day, 900 mile trip. To correct the problem, I ran a charge wire from the "coach" battery to the rear of the ERA with a connector on it. I also ran a charge wire from the Mini battery to the front of the car and attached a mating connector. Now when I go down the road, my Mini battery receives a charge from the ERA battery and the dead battery issue in gone. You can goggle and find a wiring kit to do this job complete with connector, fuse, etc, to do the job. I did mine a couple of years ago it it continues to work perfectly!
PS- in my opinion, the Patriot system is what runs down the battery, not the brake lights as they should run off the tow vehicle battery.