To Set them up for PWM control, you just navigate to Initial Setup > Engine Outputs.
You need to define the control frequency (if it was a switched output the frequency would be set to 0)

- Coolant pump GPR.jpg (31.61 KiB) Viewed 5336 times
The coolant pump control system features both an after run feature and a hold delay.

- Coolant fan GPR PWM.jpg (31.2 KiB) Viewed 5336 times
The coolant fans are the same deal, define the control frequency and plot you duty cycle target vs temp.
If the pump and fan have built in controllers, the output resource in the M1 should be connected to the control signal wire for the unit. The PDM (if a MoTeC one) should only be used for supplying constant power to the device - it is not capable of PWM output. Your control strategy logic in the PDM should be set to control when you want power to these devices, but they should only operate based on the control signal supplied to the unit.
In the GPR firmware, the control signals for the fans are only set for low side PWM control, so you may require a pullup if the control pin for the fan module is not floating with its own pullup.
The coolant fan control can be a high side PWM signal (only when using a half bridge output resource) meaning you wont require a pullup by entering negative values in the duty cycle table.