when your computer starts from power off it follows instructions written into a prom on the motherboard, these instructions also display and run the bios settings program, when you flash a bios you get a program called a flash utility or burner that often comes on a floppy, and a file of new instructions that will be copied to the prom by the burner program, so the next time you reboot (and every time after that), the new set of instructions will be followed.
Most flashes are to fix problems with the bios or in this case to add extra options to the setup pages so that you can alter something that it wasn`t possible to do before since you didn`t have the option, in this case it would add the option to disable the onboard video so that the new card could be used with no problems, IF something went wrong (like you flashed the bios prom with the wrong file by accident) then the computer would be unusable since the instructions in the bios prom would maybe crash or be looking for a boot drive called ae2q71 or something because it would be gibberish to the MOBO you had, for example calling devices that where not there etc.
So your options then would be to buy a new MOBO and plug the cpu/mem/drives etc into that or order a replacement bios and have some sad idiot from PC world lecturing you on how you invalidated the warranty and would have to pay £50 for some retard to fit the bios prom (a 5 second job), wipe half the files off your HD, lose a stick of your DDR then tell you it was a virus that wiped the HD and the case was scratched when they got it and this version always only had 64mb of ram (not that I have a low opinion of PC world employees or anything), flashing a bios can leave your hardware useless, only do so if you are sure you want to take the risk and know exactly what you are doing (and have the money in the bank to replace your MOBO in a hurry and know how to do that as well)
Mentor.
PC1: P4 hyperthreading 3ghz, 1gig mem, 2x160gig hd`s, ATI radeon 9800 pro gfx, 6 way surround sound, PC2: AMD 1.2ghz, 512mb ram, FX5200 ultra gfx, stereo 16 bit soundblaster, ups.