That's the correct way with a Perko switch. Run the stereo when you're parked off the stereo battery, switch over to the other battery to start, then switch back when you want to charge both. Realistically you should run it on only the starter battery for a bit to put the charge back into it first, then switch to all. But realistically you probably won't have any problems. They sell solenoid/isolator kits that will automatically switch it over once the starting battery gets it's charge back.