I plugged my Cyclone IV GX kit to my PCIe Expansion slot. lspci command is not listing my device. What should I do?

I just plugged in my board and expected it to show up. Let me load the reference design and see if it gets recognized.

I have on off-topic question: I get two clk signals into my FPGA -- clk125p and clk125n can I just pick anyone? or do I need to do something like this: clk = clk120p && ~clk120n?