The variable speed pump should be wired directly to power and turned off and on through it's own timer, or through your controller. The AutoPilot will not be able to wired so that it cycles on and off with the pump. Therefore, it will rely on the flow switch to turn on and off. However, it's not the best method to ensure that the cell does not turn on accidentally when there's no flow, which can cause hydrogen gas accidents.
I would suggest using the ONE SPEED PUMP mode to program the AutoPilot to cycle on and off. That is, when you program PUMP PROGRAM 1 on and off to synchronize when the pump is on, it will ensure that the unit cannot activate the cell with the pump off.
Contact me for instructions on how to do this.