In AN84868 , Acting as a master, FX3 can configure the Xilinx FPGA in Slave Serial. It also describes how FX3 firmware switches to the Slave FIFO interface after the FPGA configuration is complete. You just need the bin/image file which you would like to program the FPGA. The FX3 will take this file from the PC, and send it to the FPGA over SPI, and wait for status from the FPGA. This is done for Xilinix FPGA, if you want to program a different one, you need to check if that FPGA support SPI programming and according what are the status pins that the FPGA generates. You do not need any FPGA related driver on the PC if you have the bin/img which is needed to be programmed on the FPGA.