Adapt the example from Xilinx SP601 XTP038.pdf for your setup.
Generate BIT File:
../build/bitparse -i hexraw <your File>.bit
Generate BIN File:
../build/bitparse -i hexraw -o bin -O <your File>.bin <your File>

Spartan6:
========
At least the Multiboot Image should be generated with the bitgen Options
" -g next_config_register_write:Disable"
" -g Reset_on_err:Yes"
so that booting a partial written or corrupted multiboot image will 
result in the golden image to be booted. Otherwise only a Flash pattern 
with no valid sync pattern at the multiboot address 
(and up bitgen option TIMER_CFG = 0x10000 bytes) will use the golden image.