Contact Froggy. He is the man with this stuff and he has helped me out with my set up. You can throw a wire from the alternator to the batteries and it can only help but it will take a long ride to get any kind of charge out of them.
From what I was quoted, a 120-150 amp marine alternator is almost $1000. You can get one of these to charge the system. My stock Merc alternators are only 60 or 65 amps so a 150 amp would be a significant jump and should help a lot more than what you have. As long as you don't have twins(double the cost), it seems like a good route to go.