another thought,
on my boat I have 2 batteries, 1 starting and 1 deep cycle. I have the starting hooked up to the outboard and it also supplies power to the items that are on my control pannel, lights, wiper, horn, bilge pump. On the deep cycle, I have all my electronics and down riggers. This battery is hooked up to my kicker for charging. I don't have the batteries connected. I do have a set of inexpesive jumper cables in my boat in case I ever need to jump one to the other, but never have. Both charging systems and batteries are isolated from each other and no swithces or isolators to worry about.