I have almost the same setup as you. There are a few different ways you could wire it. I wired mine so that there are 3 pairs of batteries with 2 perko switches. This way there are 3 banks for the stereo plus the starting battery which is connected to the alternator. When I plug in the charger I switch both Perkos to off. When I'm playing the system, I'll have the first perko on 1, and second on 1. When that dies, switch the first perko to 2, when that dies switch the second perko to 2. When that dies, go home and plug in the Pro Mariner. And by dead, I mean when they hit 11.9 volts. It might sound confusing, but it's pretty simple really. Here is a diagram