Hello
I apologize but we are not familiar with the protocol needed in the SPARTAN 6, to configure or program the device, my advise would be that you contact Xilinx to give the proper instructions on how to configure/flash the device. My apologies that we are not able to help you.
Another Idea that came to my mind, it is to use the program, and flash it with Uboot into a SPI flash, that handles the FPGA, but again, we need to understand how and where in the memory it is needed the content of the FPGA.
Have a nice day