I want to start by saying I know it isn't a code problem as it was working before but after I hooked up another motor controller (from a different manufacturer) it caused my motors to briefly spin up and then stop and stall. I stopped it immediately and put 2 flyback diodes in parallel on the motors and disconnected the other speed controller but now it is producing this behavior where if I tell the left PWM to go at 100 dc and the right at 0 dc (with both enables on) it causes my ~ 10.8v voltage source to go drop to 5 volts (which is expected at full power draw). Measuring the motor leads says 0 volts AND measuring the output motor ports on the module gives 0 as well. I am really confused. I thought the voltage would only drop if it was spinning but it's not spinning and it is pulling the same amount of voltage drop under max power.
Whoa ! I bet them diodes get HOT !!!!
No, they are cold.
Then your schematic is not the same as you actual circuit you have.
That diode in effect shorts out the power supply.
If those motors can rotate in either direction then it takes 4 diodes to remove the back EMF, not two.
I looked into my motor driver and it apparently has those flyback diodes built into it
Yes and if you would have supplied details about your motor drive then that could have been eliminated first off. So remove those extra diodes you added because they are wrong.
What also would have been good is if you could have supplied a schematic that was in some way understandable.
There were two issues, being that yes, I was shorting the power supply. However, the battery was also dead. I am a complete noob at this stuff as you can tell. Why were my diodes shorting my battery?
Because a diode conducts electricity from the anode (the flat of the triangle in the symbol) to the cathode (the thin line end). You had a diode wired with the anode to the positive supply and cathode to the negative or ground of the supply. So that is a short circuit.
I think you need to look at the basics of electric circuits before you proceed because you current knowledge it not up to being to wire anything up.
Yes putting a short circuit across a battery will kill it stone dead.
Hi,
You really need to post a schematic of your working project so that others can see what had to be done.
Post a circuit diagram of your project, including power supplies, use a pen(cil) and paper and show an image of it would be fine.
Please do not use a Fritzy picture.
Thanks.. Tom... 
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