It kinda works,
I can send a value over serial to the Due and the motor moves back and forth according to the received data. Motor direction depends on the new value being greater or smaller than the actual encoder-register.
Next step is to use the step-pulses from Duets external stepper port to make it run in sync (speed control) and use the dir pin as well.
Thanks for the information. I must have read this document several times already. It summarizes the method for defining pins well.
I think I'll use the CS5 pin to ground for my application. The hiccup I've had in the literature is finding out what the supplies voltages are. Based on the referenced document, there is no PWM and I believe the output is 3.3V when triggered for CS5 pin.