What Ed said.
Best option is to install an off/1/2/both type battery switch (clock) so that you can select the battery you wish to use. For instance - and assuming both are fully charged; select battery 1 for starting the engine and running to where ever you are going. Then, if you'll be there a while and want to use stereo, etc, shut down the engine and then select battery 2. You can then run everything off batt 2 for as long as it lasts. Time to leave? Switch back to batt 1 and start the engine.
Slight correction though, If the batt switch you install does not have a built in charging circuit, and if you don't have a combiner, the alternator will not charge both batts at the same time unless the switch is set to "both". In other words, if the switch is set to "1", batt #2 will not get charged, if set to "2" batt 1 won't get charged. So, with the scenario above, once you re-start on batt 1 then simply switch to "both" so both get charged.
Companies make switches that will charge which ever batt needs to be charged regardless of the switch position, but that requires that you wire the alternator's charging output feed to the battery switch. On my '04 2400 SC3 the alt charging lead goes into the wire harness and terminates at the starter - and it's NOT easy to get to the starter to disconnect that lead and re-route it to the switch. I could have just cut the lead before it went into the harness but I hate cut/dangling/un-terminate wires so I didn't.
One other thing. If you leave your boat in the water DO NOT leave the switch in the off position. The bilge pump won't work (unless you wire it directly to the battery).