You don't have to disconnect them, even with a single charger. Just put the leads on the positive and negative of the same battery. When that one is done, put the leads on the positive and negative of the other battery. Because the circuit is completed with only one battery, the other one doesn't come into play.
As such, you can still pull 12 volts to run accessories off a 24v system. Just pull a positive and negative from one battery.
A two bank charger will have two sets of charging leads coming out of it - hook one set to one battery, and another set to the other.
As far as the transducer, I usually run all of them up the foot control cable, as opposed to the mount. At the point where the solid shaft meets the moving shaft, just give enough slack to allow the motor to turn fully in both directions, and put a piece of heat shrink at that spot.