More than likely on is designated as the Start Battery, and the other is designated as the House Battery.
Usually the battery switch is wired as [1 = Start; 2 = House].
You should start and run on the Start Battery, and once stopped, switch over to the House battery. I sit on the house battery bank even if connected to shore power. If we loose power, you want the largest battery bank possible.
Using BOTH or ALL will leave you with no way to start the engine if the battery banks are accidentally drawn down.
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