Can a person run two Batteries in parallel with these motors? Sometimes we anchor and swim several hours using the stereo and accessories. Will the alternator charge two batteries at once or should I just have a completely separate battery?
Unless you run the motor a lot at higher speeds you will not get much charging on the batteries. Best to have a spare battery and charge it when you get home. If you buy a spare battery it should be a regular marine battery and not a cranking battery. If you choose to run batteries in parallel you really need to get exact new batteries. If you hook a new one to the old one the new one will degrade faster till it matches the old one.
+1 on what Eurolarva said. A better setup would be buying a Deep Cycle battery for using the stereo etc and charging it when not on the water. If you buy a charger with a tender, you can plug it in and forget about it until next time you need it.