you have a lot going on there! I'll try to help, been thru this a hundred times. These are my opinions and suggestions only, I believe these to be a safe and positive remedy for your situation, others may disagree and that's OK, each to his own--here goes. No.1 you need 2 matching batteries, I prefer dual purpose marine batteries, preferably made in the USA. They hold up well and withstand many chargings. NO.2 A Perko 1-2-all, on/off disconnect switch. This switch does the obvious= on = off and allows you to run on battery no.1 or no.2 or both, I am a firm believer that the electricial system should be shut off at the end of the day. I want my boats main breaker-fuse box wired to bat. no.1 via disconnect switch. On this circuit is main engine, nav lites, fans, blowers, interior lites, horn ect. Battery no2 will have a second fuse/breaker box with my depth finder, downriggers. whatever other equipment you have for fishing. I isolate my batterys while I am fishing so I always have a fully charged battery to start my main motor to go home with. If you keep your boat in the water, I would install a bilge pump with a automatic float switch, wired directly to the main battery via a inline fuse. All this is really pretty simple and just common sense, if your uncomfortable with this I would consult a certified marine mechanic, hope this helps tight lines Blackie