Onboard battery charger question

In my boat, I have a dual onboard battery charger. One side is connected to
my engine battery. The other goes to my trolling motor battery. With
regards to my trolling motor, what happens if I hook up another battery in
parallel to my trolling motor battery? My trolling motor is 12V and by
hooking up in parallel, I still have 12V.

My question has to do with how the onboard charger from one side would
charge those two batteries hooked up in parallel. Is it possible that if
one battery is not as full as the other, that the charger would "cook" one
battery too long? Keep in mind that I am only talking about the two
batteries hooked up to the second output of my charger. The first output is
hooked up only to my outboard battery.

Thanks,
Jeff