elnuts;
You should only need to hook up 1 bank to 1 Battery, the second Battery will be will be charged at the same time as the first Battery, example when you are using the Trolling Motor with the to Batteries hooked up the way you have them, you will be discharging each battery at the same rate, therefore the recharging works the same, If your boat has an Electric Start on the Gas Motor and you use a 3rd battery for it, just hook the 2nd bank of the charger to that battery. If you do not have a 3rd battey, remove the connecting terminals and tape them up to avoid any possiblity of shorting out Having the Charger hooked up at the same time that the Trolling Motor is hooked will damaged the Trolling Motor. 12 volts is 12 volts no matter ware it comes from. Just make sure that you only hook positive to positive, if 24 volts get to the Trolling Motor it good by Trolling Motor.

Hope this is helpful
BKehl