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You have to implement the SPI Master in your FX3 Firmware. After booting up the FX3 you have to configure the FPGA via Slave Serial interface (similar to SPI) with the bitstream sored inside the SPI flash at higher address. With the SPI master firmware you can reprogram the FLASH with your host software. But be aware of the hardware limitation: You cannot use the hardware SPI if your GPIF is configured in 32 bit data width. Also you cannot directly let the FPGA boot from FLASH as both, the FX3 and the FPGA expects the bitstream stored at address 0 in master spi boot mode.