Battery Charging
The problem is not with the alternator, but with the voltage regulator. The typical set up on a stock boat is a conventional automotive type voltage regulator. This device allows high amp output to the batteries initially, but quickly drops the voltage back and charging a deep cycle battery becomes next to impossible. If you really want to be able to charge a deep cycle battery with your alternator, you need a multi-stage voltage regulator that operates similar to the plug in type battery chargers with at least a 3 stage charging cycle.