Hmm... I'm looking at the manual for it and it doesn't look like it is much help.
Are you running Windows? I don't suppose it specifies the model of the controller in the device manager, does it? If it does, you can just disable the PCI one and see which one is still working - that'd be the PCI Express slot.
88E8056 is the PCI Express controller. 88E8001 is the PCI one.
Incidentally, does your board have the USB header for ports 11 and 12 between the audio ports and the first PCI Express x1 slot?