I'm thinking for the logic I'd allow a pretty good sized dead zone where the motor will not make a large adjustment. Then I'd use the dual GPS to calculate a heading and if I'm moving away from the spot backwards then the controller would crank the motor all of the way over to the side that makes the most sense and make the boat do full turn with power proportional to the directional error, then slowly pull the boat into position. Once it is aligned correctly then it should be able to hold position fairly well.
It's something I'm mulling over. I need to take a look at the connections on the existing controller and see if I can basically replicate the output of that.