If your #2 battery or whatever one is wired directly to the Wallas, it's usually designated as your "house" battery. That's the one you should use at anchor then, if you run it all the way down, you've still got the #1 battery (start) to start your engine in the morning. After you start the engine, switch it to "both" and you'll charge the other one back up as you travel for the day.
Charlie