Im sure somebody else will jump in here, but here's my .02 cents.
I am assuming the one bank charger you have is a 12 volt output.
I am also assuming you leave your 2 trolling motor batteries hooked up in series.
If both of these are true, then you could leave batteries hooked up as is, and just charge them one at a time without taking them out of series before charging.
The only option to charge both at the same time, would be to tie the batteries in parallel which I have never done since I keep mine hooked up in series for my 24v trolling motor, and I am not sure if the batteries will charge as well like that vs being charged independently 1 at a time.
Sounds like a multi bank charger would eliminate some of the hassle for you down the road.
Again, just my .02 cents.