I have only ran the single fan version on a vehicle, so I can't comment on the dual fan version about any sort of PCM output issue. A pull up resistor might do the trick.

About the power wire and controlling ground versus positive switching, there is the same amount of current on the ground as there is on the positive, so keep that in mind.

I would have also used Automotive Bosch style relays, and mounted them closer to the battery and fans.