You would only need three batteries, 1 deep cycle/marine starting for the kicker and run the 'riggers.
Then 2 batteries, 1 starting for the big motor and 1 deep cycle for the remaining accessories, lights, vhf, F/F, livewell, etc. Those two batteries are kept separate through an isolater only for the reason that when the big motor is not running, you will never run down the starting battery and be stranded. However whenn the big motor is running, it will charge both of those 2.
If I can figure out how to draw some schematics for you, I'll do it a later today and post.