I have a 3 bank in-board charger. My question is my 2 trolling motor batteries are connected in series as my tm does not have a 12/24 volt switch. When each has it's own pair of leads from charger should I disconnect the jumper wire between the two tm batteries to get a full charge on each??

P.S. Part of the reason for my concern is I've heard when 2 batteries are in series the WEAK one could draw the strong one down.????

I have a minn kota charger that allows the wiring to stay the same w/out removing the jumper wires.

It has instructions on how to wire in the charger with the jumper wire attached. I have not had any problems with it charging both batts.

The charger will charge both batteries to full capacity as long as it is installed correctly. (If it wasn't installed correctly you would know due to dead batteries or blown fuses by now.)

Your concern about the weak battery is not exactly correct. When you have two batteries connected in series, the total current output will be limited by the weaker battery - but it will not harm, damage, or otherwise change the stronger battery.

Ex: I have one 200A battery in series with a 100A battery. The series combination will be limited to 100A current output, because both batteries must be passing the same amount of current. In all likelihood, the 200A battery is larger, so it will retain charge longer.

This just means it does you no good to have one big battery in series with a small battery. But they will both fully charge and one won't damage the other.

to answer your original question.....

my DualPro 3 bank does not require removal of the "jumper" cable that connects the 2 trolling batteries.
i would be surprised to find out that any charger would require batteries to be disconnected.

My setup is a 24V system, and you do not have to disconnect to charge. I leave plugged in, when not in use, and going on 4 years with my cheapest Academy batteries (about $75 each). If you do leave plugged in all the time, be sure to periodicly check the water levels, as charging causes the water to evaporate. Ran mine almost completely dry when I noticed this about 2 years ago, but still going strong. Charger is BPS XPS 5/5/5 charger.