Same situation, decided to go this way-
Existing 12v7ah battery for the Lowrance Mark-4 (located in hull behind "tackle station" in waterproof case), will be dedicated to FF/GPS only.
Utilizing the Hobie battery holder (which will be located in the rear deck hatch), I'll be adding a generic 12v9ah gel battery to power the Micro Anchor.
Reasoning- I have to strip this boat in July, and having the two power set-ups seperate will make that chore easier.
Also, I think the chance of some type of "interference" with the FF operation would be lessened by keeping the two units seperate.....but I could be way off base on that thought.