Well if the flash utility makes a bootable floppy from an image then you would just boot to the CD and go. If not, your gonna wanna make a boot disk and copy the flash utility to it. Then boot to a dos prompt with the disk and execute the utility.
MAKE SURE YOU DONT *F* with the machine while its flashing. If the power goes out or if you turn the machine off in the middle of it, chances are, you now need a new board.