Perhaps I'm somewhat confused, happens often.
I've only had 2-bank chargers that only charge the 2 deep cycle trolling motor batteries, 10 amps.
The cranking battery is independently charged at home in the garage regardless of how much I've run the motor.
There is quite a bit of demand put on the cranking battery besides cranking the motor.......graphs, live well, running and console lighting, bilge.
A long day of fishing my cranking battery is exhausted and I don't rely on the alternator for a full charge.
Note:
Your 24V trolling motor batteries are not being charged on the water by the alternator.