Here's an isolator/relay that you can use to break the circuit between your stereo batteries and your starting battery:
http://www.stingerelectronics.com/productDetails.aspx?delineate=735&CategoryID=12&Pa rentID=1 That only allows the stereo batteries to be connected to the alternator or starting battery to charge when the ignition key is on.... The only drawback is that I don't think you're alternator will handle 2 extra batteries in addition to the first battery too well. You may consider upgrading to a high-output alternator.
For charging when the boat is trailered or docked, you can use one of these per battery. You can hard-wire them in and just plug an extension cord into it.
http://www.stingerelectronics.com/productDetails.aspx?delineate=735&CategoryID=12&Pa rentID=1 I always use the Stinger batteries in my installs and my own boat. They have a 2-year warranty so if you kill them in the first year, you can get them replaced for nothing. The SP1500D and SP1700 are ideal for boats. With 2 SP1500's in mine, I can play for 2 days in the party cove from start to finish and still have reserve time on the batteries.