This is a neat idea. Here is something I found while researching the subject of steering a simple trolling motor. http://www.duckworksbbs.com/plans/simpson/steering/ElectricSteering.pdf
This guy made his own steering system from scratch. You could use a motor shield on an arduino to drive it without any trouble. It shouldn't be much trouble to hack the controls in the top end of your trolling motor. Keep in mind that you will likely need to use relays so that you don't burn up your arduino with an overvoltage. You could use a small thumb joystick for the steering, and a 3 position switch for the forward/reverse/off. You should be able to find lots of instructions for driving motors and servos with joysticks and switches. I'd be curious to see this project if you choose to pursue it. I'm sure some other people would too.