Yes you can do this. Use the M584 command (see [reprap.org]) to re-map the drive motors in config.g, and put your M906 command after it. You do not need to change PanelDue or DWC settings.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].
