You can charge them individually, likely without disconnecting them from the trolling motor. Just connect the charge to the first battery pos and negative. After it is charged, move the charger to the second battery pos and negative posts. If the trolling motor is turned on during charging, you will have a short circuit.
However, if you want to charge them both at the same time, you must disconnect the lead between the first battery negative post and the second battery positive post.
Then connect the charger to the first battery pos and neg and jumper from the first battery pos post to the second battery pos post, and from the first battery neg post to the second battery neg post. Make sure to follow the polarity of the charger.
If you install a battery switch, you can probably switch from parallel for charging to series for running the trolling motor, easily.
