Hi,
the FPGA programming devices (EPCS, ECPQ) can be programmed in two basic ways:
- you generate a .jic-file, connect to the FPGA via JTAG (USB-Blaster), and program the file into the flash through the FPGA
- you generate a .rpd-file, and program it into the flash using an SPI master
If you're looking for a method that doesn't involve a USB-Blaster, I recommend the second option. All you need is an SPI master. The manual of the EPCS and EPCQ reveal all commands you need (bulk erase, write data, read status, additionally read data to verify if you like). Also, you must put the FPGA into reset before you can access the flash memory. I recommend to read the manual of the EPCS or EPCQ (only a few pages), and the section about configuration in the corresponding FPGA handbook (a few dozen pages).
I think it is also possible to do the JTAG method manually, I think there's some JEDEC standard or something, but it'll be definitely more complicated.
Best regards,
GooGooCluster