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I do the same, start and run on both batteries. But when at anchor fishing for a long period of time switch to 1 battery to run accessories, like fish finder, radios, gps, lighting at night, saving a fully charged battery for starting. Also, to prevent fires when not using the boat, shut it completely off, to prevent something shorting out. Your bilge pump should be wired directly to the battery so it always gets power even with the switch off. Also don't change the switch with the engine running.