Is one of your batteries actually going flat?
If so, it sounds like you have a problem that needs to be sorted out rather than a set up that needs changing.
Battery in poor condition?
Faulty equipment drawing large current?
Partial short circuit somewhere?
If your batteries aren't going flat then I wouldn't worry.
My current boat has two batteries - but only ever use one at a time for both starting and electronics. Always leave the plotter and sounder running if leaving the boat for a couple of hours and heve never had any problems.
Previous boat only had one battery and again no problems.