I used a Marlec charge controller, that had two separate charge outputs, one of which I used for the domestic house batteries, the other was used to charge a totally separate bank of batteries used in my case for an electronic antifouling system that was switched on when the boat was launched in the spring, and off when the boat was hauled out in the autumn. The engine start battery looked after itself, though I had a wired in emergency start changeover system that I could use in event of the engine start battery going down. The boat was kept on a swing mooring so no mains power during the season, and it all worked well.