This is a total SWAG since I know nothing about the motor driver board you have. But... I am presuming that the 5V wire you mention is NOT providing the voltage/current for the motor itself, but rather is used for the step/direction interface. If that is indeed the case, and there is a separate connector/wires for motor power, then I would suggest connecting the PMDX-126's "PC+5V" to the driver's "+" wire, the "PCgnd" to the "-" wire. I am guessing the step and direction inputs are the other two wires, "D" and "C", but it is anyone's guess which is which. So pick a connection - map one to "step" and one to "dir". See what happens when you try to jog that motor. If it moves back and forth, you are done. If you get one "click" each time you attempt to jog back and forth, swap the step and direction pins and try again.