Crude drawing of back of Perko.
Hook positive of battery one to "1" and positive of battery two to "2". All stereo, starter, and accessory power to "3".
Hook negative of battery one to battery two and then to negative of starter. Also, all stereo and accessory can be grounded to either negative battery post as they are connected anyway.
Turn dial on front of Perko to "1" to draw from/charge battery one, "2" to draw from/charge battery two, "all" to draw from/charge both, and "off" to disconnect system completely.
If you want multiple batteries for stereo, then hook starter battery to "1" and then hook all positives from stereo batteries to "2" (all negatives can still be connected across all batteries)