Hi,
The problem is in the recharge process. If you have a 200 amp hour battery, say group 8D cart batteries in series for a total of 24 volts, and recharge with a 25 amp charger, it 'should' charge all the batteries at the same rate. So if all are discharged by say 50 amp hours, 2 hours of recharge will charge them all fully. However if you have been running a 12 volt stereo on 12 volts of one 'battery' that might be -80 amp hours, while the other battery might be -50 amp hours.
Sure it would be 'possible' to recharge. In this case, you add 80 amp hours to all the batteries. The battery at -80 amp hours will fully charge, while the 12 volt battery at -50 amp hours will get 80 amp hours, and change all that extra amp hours into boiling water and gas vapors. It will be hard on the second 12 volt battery. Even worse might be if the first battery (that powered the 12 volt load) would not get fully charged.
Two ways that can combat this. Put equal loads on each 12 volt battery, so say your right headlight is on battery #1, while a equal load light #2 is on battery #2. Or run the stereo on battery #1 for a hour, then battery #2 for a hour. Yet the second way can lead to one battery being discharged more than the other.
Two better ways to handle this. One is a 24 volt inverter powering a 12 volt battery charger. It is not that expensive, and will get the job done, even with a 40 - 60 amp 12 volt load.
The second way is a 24 volt to 12 volt converter. I have no idea how expensive they are, and how many amps each will carry.
A third way is to install a solar system to provide recharge of the 12 volt battery. Then use the 24 volt system to recharge the 24 volt battery bank. I would recommend running the inverter on the 24 volt system, as the wiring can be much smaller.
Good luck,
Fred.