You have a slot for an EEPROM on the FX3 DVK. This can be used in any case.
Using the GPIF II connector available on the DVK, you should be able to connect to either camera or an FPGA. You can not connect both at the same time.
Could you please let me know the use case of connecting both FPGA and camera to the GPIF II at the same time. Also please let me know the revision of the FX3 DVK that you have.