I have a NZXT Phantom 410 and the built-in fans aren't working (that were already wired for me) and I have read a few articles on this same problem but none that address this problem with my motherboard (ASUS A88X-PRO).
What sort of an issue are you facing? Are you speaking of the molex connector that is required by the built in fan controller or the fans themselves not working. You can have them hooked up to your fan headers found on your motherboard although the fans are 3 pin headers they will be compatible.