We are running a 36 volt trolling motor at work. The larger the thrust, the more power they consume. In order keep the motors a reasonable size, they run higher voltage and lower current - hence the 36 volt in my case. I have a 3 battery 20 amp charger (total of 20 amps, divided as needed across the batteries) with all isolated outputs. It can charge 3 batteries in series, parallel, or isolated.
There are boxes which will rebalance 24 volt packs, so all you do is center tap them, and go. You can charge and/or discharge the 12 volt, and the box will maintain the 24 volt pack balanced, and at twice the voltage of the 12 volt battery. The battery you are using takes most of the load, the second one is either charged, or discharged to back up the first one at whatever the current limit of the box is, usually 10-20 amps on the 12 volt side.