Hi,
I might be wrong but I believe that you should be able to run the Raid card in the second slot as PCIe is backwards compatible.
However, if you are using a Graphics card in the 1st PCIe slot you might notice some graphics issues, as the bandwidth will drop to 8x's rather than the 16x's that it runs at if only 1 PCIe card is used as the 2 slots share bandwidth when they are both used.
If you are only using the on-board graphics then I don't think you should have a problem.