The first thing you can do to prevent rust is to empty the water heater when not in use. Install a bypass kit, secure the power, and drain the tank when it isn't going to be used. The second thing kind of goes along with the first, that is, don't let the water just set in the tank, cycle the water through on a regular basis. The point of these two actions is to prevent letting the water just sit in the tank.
Third, the way the water heaters are mounted flush to the deck allows water to become trapped underneath and rust the housing from the outside. building up mounting points that slightly elevates the water heater base will allow the deck to completely dry underneath.
Finally, if you don't need water heated by the engine, simply disconnect that side and only use electric to generate hot water. This really only works well for folks that only use hot water while on shore power or run a generator.
