I think there's a spot of confusion here about 'series' and 'parallel'.
As grasshopper says, you can charge batteries that are in series 'till the cows come home. By the way, 'series' means that power is supplied from only one terminal on each of the batteries, the outer ends being connected. So, for instance, the red wire on the ESC goes to + on one of the batteries. The - terminal on that battery goes to + on the other battery. The - on that battery goes to the black wire on the esc. Confused?
Never be tempted to connect batteries in parallel ie. + to + and - to -. As has been said already, all batteries exhibit small differences. This why when you connect a jump start battery on your car there is often a small flash as current rushes from the 'good' to the 'bad' battery. You don't want that in a model boat. Worse, if one of the batteries should fail, the resulting current flow will soon turn your pride and joy into a blazing wreck!