I ALWAYS use either battery one or two but not both when running the engine. Should you lose your belt or alternator output while motoring...you will drain the battery the switch is turned to...making it impossible to restart the engine after repairs. If you have the switch at both...you wil drain all. Ask me how I know!
My suggestion would be to charge your batteries at the dock and start and run on your house bank. Get an echo charger for your start battery but otherwise hold it in reserve for emergencies.