You need to either swap out the internal regulation or consider external regulation. Then you can charge the batteries at set points you determine.
Of course, if you have the stock 35 amp Motorola or Delco alternators, you're not going to charge anything particularly quickly. I think of the alternator on a direct-drive Atomic 4 as being fit to run nav lights under motor at night, and not a whole lot else.
You can always shorten and "up gauge" your wiring
, too, to get maximum pop out of the juice you are making, but I would say if you have charging
issues, go to a pair of Group 27s or even Group 31s, upsize to a 55 amp alt, and monitor
state of charge with some sort of regulation when 14.2 needs to go to 13.4 or whatever equals "float" on this boat.