Question on using on board battery chargers

On my 12 volt trolling motor batteries of which I have 2 in a series hooked up, can I install a 2 bank 12 or 20 amp on board charger that is designed as a 2 bank charger and charge both batteries just using One bank and not use the other bank of the charger at all? I only want to hook up one bank as not to have to contuially disconnect the positive wire to both batteries as that is a pita. I previously hooked up a 4 amp single bank on board charger to both batteries and it took the single bank 4 amp after using the batteries only 4.5 hrs of cranking over 17 hrs to charge both fully. I can hook my portable battery charger up with alligator clips and if I set it on 2 amp charge it will charge both batteries over night. If I go to a 12 or 20 amp 2 bank and only connect 1 bank, will a 12 or 20 amp charge both batteries in say, a 8 hr. nite? Or do I stay with using a portable charger with alligator clips which is faster? Most single bank on board chargers are only 6 amps big that I am finding without spending a ton of money. I am also hooking the chargers up positive on the A battery positive post and neg. on the B battery neg. post for a equal charge to both. MK V2 55 thrust trolling motor is only thing hooked up to the 2 batteries in the front of my Jon boat.

The best way is....get a charger with a bank for every battery you have...on the series batterys....you really do not have to un hook anything...you connect a bank to each battery....thats it....Yes you can charge two batterys with one bank but...it going to take twice as long....example if a 5 amp charger...its just like charging with 2 and a half amps. I have a three bank charger.....each bank is 10 amps....I have two big group 31 batterys in series and then my group 27 starting battery. I have a ten amp bank connected to each one. I can pull crankbaits all day long the TM batterys will charge up over night. It is going to cost some money to get a good onboard charger and do it right....but it will pay off in the long run.

I know you can charge 2 batteries with a 2 bank charger when they are hooked together 24 volts for running a 24 volt trolling motor, but I am running a 12 volt trolling motor and my 2 batteries are hooked together making one larger 12 volt in a series (pros wire to pos, neg. to neg.) and your telling me I can hook a 2 bank charger ( one bank each) to each battery while in 12 volt without disconnecting anything? And the charger will charge each battery? That is why I was going to,spend 150-200.00 for a 2 bank 12 or 20" amp charger and only hooking one bank maybe instead of the 2 knowing one large bank would take alittle longer in,charging, but if using 20 amps would be maybe sufficiently enough to charge both over nite when trolling 6-8 hrs a day. 4 bank single just takes too long so I put it on my engine battery.

Yep....Your batterys are wired in parallel for 12 volts You can connect a bank to each one....A twenty amp two bank charger should do it....thats 10 amps per bank

I am wired like you are on 12 volt. I run a 12-2 charger just like G says and it charges fine most days. Takes a little longer if I run it all day hard. The 20 should be more than sufficient to do what you want.

Thanks, 20 amp 2 bank charger is ordered.