For the 4 PCI-e connectors onboard (2 of PCI-e x16 & 2 of PCI-e x8). They auto sense the add-on devices & supports one of the following configuration (maximum)
Intel ICH south bridge should be set at auto, please see below manual for details
http://www.supermicro.com/manuals/motherboard/7500/MNL-1178.pdf
page 5-13.