Just to clear something up -- both of these batteries were charged 100% before you put in the water?
Something is draining them and draining them fast... and if you know the batteries are good (how old are they?) and you know the alternator is good then you don't have too many options. Is this an old alternator with an external regulator? When I bought my boat they had it wired wrong and the same thing was happening. I switched to a 1-wire alternator from DB Electrical and have never had another problem. I think they sell a 105 amp marine alternator for ~$120.
If it's not an alternator wiring problem, though, this isn't going to solve anything. Is it possible that your battery charger is faulty? I'm thinking it may have charged your battery enough to get the boat started but the stock alternator is pretty weak and isn't going to do much more than keep it charged while running -- unless you're running for hours, I wouldn't expect your alternator to recharge a nearly-dead battery.
Former owner of a 1987 Supra Saltare. Current owner of a Malibu 23LSV.