Hi Jayson,
You program the SPROM via JTAG with IMPACT. You can also program them with a programmer before fitting it on the board.
What we usually do is FPGA + re-programmable PROM + JTAG + Impact for prototypes. After testing the board and being happy with your FPGA code then the boards go to manufacturing and the PROM is replaced for an OTP (one-time-programmable) PROM (which is much cheaper) and is preprogrammed with a programmer before being fitted to the board.
Regards,
Maestor