Parallel connection of the two 12V batteries is 100% correct as all have stated. Positive to positive. Negative to negative. This allows any energy requiring device to draw from one battery or the other or both and thus each of them drain at the same time. Since the electrons only get energized by the battery they come from, there is NO doubling in voltage and no chance of damaging any 12V device. This is exactly what we do when we boost a car.
Another option is to simply have the spare battery on board (but you will have to re-charge it once in a while) and use it only in an emergency or swap the batteries frequently. This second option never lets you down (again if the spare battery is fully charged of course.) The only trouble with a parallel connection is (even though you have twice the energy storage) an unusual drain would run both batteries down at the same time and you might not know about it until you end up with two dead batteries.
Under normal use with a fully functional charging system and no unusual drain, you really only use the battery to start the machine and once the ski is started the battery does not drain any more ( in fact it recharges) so a second battery should not be needed. Having the spare battery for the rare situation where the charging system is not working properly is a nice failsafe. Esp. if it happens on surf trips. But if you are close to the launch or with a friend with a tow line, why add unnecessary weight?
