I have mine wired through the stock wireing. I just clipped the wires about an inch away from the fan (so they can be re-used if need be) and connected them the exact way the stocks were wired.
I even use the thermal resistor/relstat still. What it does basically, is when it gets warmed up, it allows more voltage to go to the fan to increase the speed.
This would be a simple 2 wire cut and splice per fan, with a little creative thinking to re-mount everything.