Yes, that's fine. The motor power would come from the 12v battery, and logic power from the 9v (at least, from what I can tell from your diagram).
It should send the motor into full speed in one direction.
Yeah everything looked solid about that setup. Tested the connection first directly from battery to motor: wires, fuses, battery, motor all good.
Gave it a shot through the motor controller.. nothing. Could be my soldering or something really up with the motor controller. Any suggestions?
As an update, I did get the motor controller circuit to respond correctly, connecting 12V battery across +/- terminals and battery across A/B, 12V to VIN and GND to the logic ground, I can use test buttons A and B to light the LED's corresponding to CW and CCW testing enabled. Also supplying 5V to both PWM and DIR will light up B. All these results were expected.
However, the motor won't budge. I tried testing the current across the motor and battery leads at the motor controller, and blew several fuses in the the process. Am I testing that wrongly? Do I need a clamp tester instead?
*Update again: test current in series, test voltage in parallel. Solved the problem of blowing the fuses. Still can't pull a reading, going to get my hands on a clamp meter tomorrow.