Chowder I run a Perko battery switch on my 2 battery set up. I leave it on the both position and always have no problems running all my stuff all day long. The alternator keeps both batteries charged up while fishing. No issues at all. Like mentioned before, don't switch it while the motor is running, you will blow up your alternator.
Just make sure you have 2 good batteries when you start out, as a week one will drain the good one.
RR