Are the wire colors BRN/ORG, DK BLUE, BLACK?
http://www.autozone.com/images/cds/g...3d800d30ad.gif
The diagram is not overly helpful due to the control module – an actual manual might help. So the question is what voltage hits each of the 2 circuits and when. Do they both get full 12v (likely), or does low speed get fewer volts (like low speed in an LS1 car)? Is only one circuit energized at a time (is voltage 0 at the low speed when the high is energized?)
The easy way around is just use high speed. There may be a few ways to have variable speeds, but answering those questions might come in handy. Multiple speeds requires multiple relays and fan switches, or a progressive controller.