It has been a while for me, but if I am not mistaken, you define the pins that are used, and identify them in the set-up of Mach. Then when Mach goes to output a spindle comand, it sends the signal to the pins you defined in the set-up table and the output board does the rest, provided it is plugged into the pins you told Mach to use. If I recall correctly, it is all up to you.
Sorry for all the complicated technical mumbo-jumbo...
Scott
Consistency is a good thing....unless you're consistently an idiot.