About Fly back diodes and motors
Your pics aren't showing, but I'm assuming you have something that resembles an H-Bridge for your motor. If so, you should connect your diodes like in this schematic:



In this schematic, you can ignore the MOSFETs on the left and right side. The wire off the top is the battery positive, the bottom is ground.

This may look like you're creating a short, but you're not. Instead, you're providing somewhere for the potentially massive flyback current to go when the motor stops or changes direction.