In order to charge them both you would have to bypass or remove the selector switch and hook your batteries together in parallel. (Postive to Positve and Negative to Negative) Then just hook the one bank from your charger to
ONE battery and the other will charge right along with it. (Your motor will also maintain them both when it's running. (
CAUTION: Do not hook them up in series(Pos to Neg) as you will then have a 24 volt system) 
Another option would be to just hook them together when you want to charge them and disconnect them when you're ready to go on the water.
If it were me, I think I would hook up the third bank to the spare battery and let the motor take care of the primary battery. If the primary dies, just flip the switch and you've got a fresh battery ready to go.
I hope this helped.