Re: trying to set up stereo on seperate battery from engine.
You could install another battery in parallel which will give you more juice, but you still run the risk of draining them to the point that you could not start the boat (haven't run the numbers on how long that would actually take).
When I installed a stereo, I had the same fear over draining the cranking battery. I installed the add-a-battery system (Blue Sea Systems #7650) and couldn't be happier. This kit comes with a relay and a switch. The relay is what will help your situation, but I would recommend the kit since it's not much more $$$ and the switch is well worth it (don't have to mess with the battery terminals to disconnect the battery). The benefit of such a system is that when the motor is off, the batteries are isolated so the stereo drains the accessory battery and the cranking battery stays fresh to start the motor. When the motor is running, the relay senses a charging condition and connects the batteries in parallel so they both charge. The downside is you will have to fab up some battery cables (you could buy them, but they will be pricey... surprise).
If you really want to alleviate the battery juice paranoia, install a volt gauge to monitor one or both of the batteries.