Motorguide 6700 Issues

Hoping I can find a bit of wisdom. I purchased a 2003 Nitro 19' about a month ago and it came with a MG 6700 Pro Series. All batteries were disconnected so the seller (employee of owner) helped me hook it up to ensure the trolling motor worked appropriately. Took it out on the water and although it worked, felt extremely sluggish in rabbit mode getting me across the resevoir to a line where we could troll and fish (but we got there eventually and in slow speed don't really notice an issue).

Checked forums and saw how to measure voltage at the batteries and realized when I measured across the (2) that were seemingly in series they were in fact not (1 measured 12.3 after a day of use other remained 12.6/7 when measured individually). I rearranged the jumper and now am getting 25.6V across them. I plugged in and hit the MOM pedal and the propeller seems to be immensely faster than before I corrected the jumper. 

When I take the cover plate off to get behind the female plug to measure the voltage at the trolling motor I'm only measuring 12.5 volts though and I don't understand how to correct that. The motor is surely faster than it was before I made the switch but if it's measuring 12V then it seems the series voltage isn't really getting to the motor.

Is there any way I can confirm the series voltage is 1) wired properly (which I'm thinking it is since the 25.6V is in line with series measurements) and 2) that I'm not going to burn up a motor because I did something dumb?

The wiring back from the TM goes into (2) 50A breakers that then go into a Guest Model 2611 (2) bank charger and (2) Interstate deep cycle batteries (each positive has a 20A glass fuze wired into it) if any of this helps. Thanks in advance!