I am not familiar with that controller. However, I suspect you could likely run it to the low-speed fans and just put a manual over-ride relay to kick on the high speed if you ever need to.

I wired my car for the Contour fans and have high and low speed relays based off of ECU control. You could also get something like a Derale PWM controller, hook it to the high speed circuit and vary it's speed via Pulse-Width Modulation.