Take a look here:
According to this help page, having two controllers sometimes means each one controls a different set of connections on the motherboard. There is also the possibility that one may have different capabilities than the other (raid5). Your best bet is your mobo or system manual and then next would be the manufacturers site, probably a forum where you can ask specific questions about which controller does what. If one has raid5 and you determine you don't need that then use the other.