A 20 amp (for example) 2 bank charger doesn't have 2 separate 10 amp chargers built in, it's ONE 20 amp charger with 2 separate outputs. So there's always a full 20 amps available on either side of the charger. Example, you drive out into the lake a half mile, anchor up and run your 2 aux batteries dead playing the stereo all day. The half mile ride back won't charge the 2 dead batteries, but the start battery will be full-up. When you connect your 2-bank charger to these 2 banks of batteries, about 19 amps of the charger will be charging the dead batteries while 1 amp will trickle charging the start battery.
Same applies with charging the OP's 2 batteries, it's completely pointless to go to the trouble of disconnecting 2 batteries just to connect 2 separate charging cables from the same charger that has the same net output.
As for "what if one battery is shorted", it's entirely likely you'll know this before ever turning on the charger because both batteries will be dead. Fastest way to figure out which one IS dead is to charge both at once for about 10 minutes. Disconnect them from each other and check the voltage of each, the good battery will have lots more voltage than the bad one. Replace it and go boating!
