You could easily achieve this with an Arduino, some simple code, a relay, extra battery etc.
Having just typed the previous line I am now thinking of voltage drop with high current draw, perhaps better to also monitor power drawn from battery since recharge. You could also have an audible/visual alarm that battery one was exhausted and you where running on reserve or you could end up with battery 2 exhausted and the boat still in the middle of the lake!
I have never done this with an Arduino but up for the joint challenge if your interested - rough cost for kit £15 - £20
Jonathan