Well Kraig already answered your one question w/ the isolator system.
To answer your last question, Deep Cycles can have enough power to start a boat. Just depends on the battery you get.
Keep in mind that if you end up draining your deep cycles low enough and keep trying to charge them with just your alt. your gonna do one of two things. Kill your alternator, or kill your battery. Even if you have an upgraded alternator, your batteries are not designed to take a constant bulk charge.
Either learn to take them out, or install an onboard charger.