So, I have two trolling motor batteries. I put my single charger on one battery at a time. Is this right or am I  wrong in doing this?

You're good 

So, I have two trolling motor batteries. I put my single charger on one battery at a time. Is this right or am I  wrong in doing this?

 

 

Perfect! 

 

It won't work. Think about it. A 36v trolling motor will have battery #1 with + lead connected to motor and - lead connected to + lead of battery #2 which will have - lead connected to + lead of battery # 3 and - lead connected to the trolling motor. If you connect the charger leads to the + and - leads on battery #1 there is no way the other 2 batteries will charge. Theoretically, if the batteries were wired in parallel, it may work, but I think you would at least triple the charging time if not more.  

 

That's what I was thinking, thanks for confirming. My previous boat had a 24 V trolling motor and the batteries were hooked up to two different banks. A person that works for the company that's building my boat was trying to say differently. 

 

I have a pro sport 12 with a deep cycle battery for the trolling motor and a marine for the starter of the OB.  Since I have to store the boat at a storage facility, can I plug in the charger and leave it plugged in until I go back out fishing (2 -3 weeks in between)?  I don't want to have a problem with damaging the batteries by keeping the charger plugged in all the time if it isn't safe to do so.  Thanks for the help

 

 

 

If it were set up that way, one bank charging three in a series, would it just result in a very slow charge? Or would other problems arise?

 

 

One 12V bank is not going to charge a 36 V battery. Three 12 V batteries in series is 36V.

 

A multi-bank charger is 12V per bank, there is no 36V output. You connect each bank to a battery and they get charged at the charger rate per bank at a little over 12V each.-typically 13-14 volts.

It doesn't make any difference what device is connected to the batteries a long as they are separate or in series, it is still separate 12 V batteries changed individually.