I had Allen tune for my e-fans, but I have not hooked it up so the PCM will run the fans. I am still letting the Flex-a-lite VSC controll them. However, I have some free time and want to hook the PCM to the e-fans. How do I go about it, would I use the VSC as a relay somehow?

 

I would ditch the VSC and electronics from Flex-a-lite altogether. Allen makes a relay kit that plugs into PCM blue #42 for fan one and taps the A/C signal for fan two.

You can easily convert that kit to dual pcm driven fans (both on at the same time) by attaching the wire that hooks up to the A/C lead to the white wire on the PCM relay and the ground wire on the A/C relay to the PCM pin 42 wire.