Can you give more details? Have you downloaded any PCIe based design on to the FPGA in the kit? If the FPGA in the board is not programmed , ie, blank, the PCIe kit/card will not ge detected. For the kit to get detected, you need to have a PCIe based design running in the FPGA, like an PCIe End Point based design.
Try and download example designs for your kit from the Intel site and follow the steps given.
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?
Those are the LVDS clocks for the PCIe. These two clocks will be converted internally by the LVDS IOB to a single-ended clk125 internally. You can use this clock for the rest of the logic in your design.