You could wire the two stock relays to control one fan each by having the ECM trigger both factory relays and eliminate the high speed switch in the intake manifold.
Run the dark green wire from ECM controlled relay over to the other stock relay and eliminate the dark green/yellow striped wire.
At the plug wire one fan to the blk/pink and blk/red wire and ground them both well.
Both will come on when the chip programmed temp. is reached.
You probably would need to know the noise level when they both come on, physical dimensions and cfm's, as well as the cooling level with what you are using for radiator, motor, shrouding, etc., before you decide how it should be finally wired.
Lo/Hi operation with a lower intake manifold sensor may also be the way to go, hypertech I believe makes 3/8" NPT temp. sensors that fit the car.