There are two things needed to mine with the X6500: the miner software and the FPGA firmware. The software runs on a host computer, which the FPGA miner is plugged into. The software handles getting new work from the pool, sending it to the FPGAs, and sending back the results to the pool. The firmware is the FPGA configuration file, also called a bitstream. This needs to be loaded onto each FPGA every time the board is powered up.
The recommended mining software for the X6500 is the Modular Python Bitcoin Miner. MPBM is written in Python, and runs on Windows, Linux, Mac, and some users have even run it on a router or Arm computer. MPBM is open source and available on Github.
Read the installation guides for Windows or Linux here. You might find help installing MPBM on other operating systems in the Github wiki or in the Bitcointalk forum thread.
Once you have MPBM installed, read the MPBM Usage Guide for a description of the configuration options, and get mining!
If you have problems with MPBM, or are just the curious type, you may want to take a look at x6500-miner. While x6500-miner should still work, it is not as actively maintained as MPBM. For reference, the x6500-miner instructions are maintained here.