I forgot I put up some additional images of the inside of the navigation box over here: http://discuss.bluerobotics.com/t/mapping-results-from-a-rugged-arduboat/515
Your best bet is to start going through the ArduRover documentation and go from there. There are various setups and control methods available so pick something you think will work for you and go from there.
At a minimum, get a Pixhawk kit, a GPS module, a telemetry radio, and whatever thruster/ESC combo you would like. I bought pretty much everything off Amazon, so there isn't anything too exotic.
I'm on here quite freqently, so I'm happy to help get you started. Boats are a great way to get started into autonomous systems...fewer things to run into and you won't lose thousands of dollars in a crash.