I would use the alternator to only charge the cranking battery. Most boats don't run enough on the water to charge the cranking battery back to what the fish finder pulled it down to. I know mine doesn't. A short, cheap set of jumper cables would let you crank the boat with your trolling battery in an emergency situation without having to unhook things.

If my people, who are called by my name, will humble themselves and pray and seek my face and turn from their wicked ways, then will I hear from heaven and will forgive their sin and will heal their land. 2 Chronicles 7:14