Never switch the batteries with the engine running or you will kill the alternator.
It is a good idea to have shore power connected when off the boat and a trickle charger in the circuit. That will keep the batteries up. Buy two different batteries, a marine starting battery for #1 and a marine deep cycle battery for #2. Drive on battery #1 and, after shut down, switch to Battery#2 for accessories while you are floating, at anchor, etc. Once back at your dock, shut both batteries off and plug in the shore power. This is a good job for a qualified marine electrician.
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