I agree with above post as far a deep cycle batteries are concerned. A typical alternator will either ruin the battery or the alternator over time. Buy two of the largest group size that will fit in the battery boxes/trays.
The higher the A/hr and cranking amps the better.
On another related note, don't switch the battery switch while the engine is running. This can hurt the alternator's regulator and other electronic devices on board.
What I recommend to boaters is to put the switch on "ALL" to get the boat started and to your destination like the beach etc.. This gives maximum amp delivery and allows the batts to charge en-route to the destination. When you arrive at the destination, with engine stopped, switch to batt "2" to run the stereo and accessories while beached/anchored. This will prevent you from running both batteries down and un-able to start the engine.
One last note. The alternator will not charge a dead battery for long. Boat alternators aren't that powerful (amp wise) and will run at max output trying to charge a dead battery. This WILL overheat the output terminal on the alternator and ruin it. Ask me how many marine alternators I've changed due to this.