M106 P0 S(0-255) will control FAN0, and M106 P1 S(0-255) will control FAN1. However, FAN1 is in thermostatic mode by default. If you want to use it as a normal controllable fan, you need to disable thermostatic mode by sending M106 P1 H-1.
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].
