Unfortunately, I don't think there is a way to choose this on most boards. Usually you can only pick from PCI/PCIe/AGP/Onboard but not which actual PCIe. In my experience, it is the closest one to the cpu which has a display connected.
Good luck.
Actually, a lot of motherboards, so let you choose which individual slot to use. On mine, they're labeled as PEG1, PEG2, etc.