Ed,
The way my boat is wired the solar panel maintains all 4 batteries (2 house, engine start and thruster) at the same voltage. All last winter the boat sat for 5 months and this past boatinng season I never hooked up shore power to charge the batteries while the boat was not being used. The first thing I always check when visiting the boat is the battery voltage at the panel. All batteries always have voltage levels above 13 volts within 1 or 2 hunderds of a volt between batteries.
Not knowing the details of how our boats are wired I would disconnect the negative lead of each battery being charged by a portable charger. There may be a better way to do it, but that would be my approach to charging each battery independently. Since I have a portable generator if I need to charge the batteries I would connected the generator into shore power. However, in my case the solar panel has done such a good job maintaining the batteries there has been no need to use the generator, even with the boat sitting for 5 months.
Richard