You can refer to the Designing with EZ-USB FX3 Slave FIFO Interface Application note in which an Xilinx Spartan 6 FPGA is interfaced with FX3 in slave FIFO mode, where the FPGA acts as a master and controls the FX3. The application note also defines the FPGA State Machine for streaming data.
Follow up to that. I'm using a different development board than they were in the example. I'm having issues mapping the FMC connector pins to the signals on the FX3 board. Is there an easy reference for finding out what corresponds to what or do I need to go through it pin by pin?