This message was posted on behalf of Intel Corporation
Thanks for posting in our forum.
Regarding your question, you can go ahead and try the other PCIe slot, it should works as we verified in the motherboard's manual, worse case scenario, it won't boot. As for the manual, here is the link for the manual and on page 29 it shows you the setup for the expansion slot configuration.
Please let us know if you need any further assistance.