[Runtimemicro] has the answer, at least if you are writing PWM code for the Arduino. Their free application lets you set a few parameters, visually see the results, and then generates code for you.

What Are PWM Pins? The Arduino Mega's PWM pins are digital output pins located on D2 to D13 and D44 to D46, coming to a total of 15.

Lastly on that connector is the spindle output and, just like the 36V fan output, the connections are: +ve directly connected to the 36V power input and -ve modulated to 0V from the cnc domain by ...