OK, in the case of your charger, it would be fine to charge it with one set hooked to each battery. Actually, that will give you a good even charge. West Marine/BoatUS probably won't stock the 24v pumps, but they can get them for you in a day or two (around here anyway). I'm very cautious when it comes to my boating equipment. I would worry if there was anything (like a converter) between my bilge pump and its power. You'll be much better off set up like that. Your boat seems to be a pretty neat project.

Anyway, to really answer your posted question, it is possible to run the same batteries in series and parallel. This is done in 4 battery and higher setups (not in 2). Eg. You could buy two more 12v batteries, connect them together serially, and then make a parallel connection between your new pair and old pair for an end result of 24v with twice the reserve.

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1982 Mercedes-Benz 300CD
1982 Mercedes-Benz 240D - stick