So it's tied to the PCIe bus - how do you interact with your FPGA once you programmed it - are there general drivers you can use, or do you also have to create a linux driver to talk to your FPGA ?
Xilinx provide software drivers and IP for PCIe DMA and memory mapped interfaces. These are fairly easy to integrate (probably not the best for latency though - I've developed my own but I require a specific use case - low latency but don't care about bandwidth).