I apologize if my questions are less than professional, but I am a novice when it comes to outboard motors. My boat has 2 batteries at the stern. I beleive that one is soley for outboard and they other runs the bilge, lights, and live well. Does the battery for the outboard need to be charged or does the outboards have an alternator that keeps the battery charged? I also have a place near the bow for a third battery, which would be for the trolling motor(once I get one).

Is there such a thing as a deep cycle battery charger or does any typical 12v battery charger work?

While most outboards have an alternator to recharge the batteries, it never hurts to "top them off".  Most of the better chargers will have a switch for charging deep-cycle batteries.