Just don't do anything stupid and it should go fine. I update my BIOS all the time. It's probably safer to use the MS-DOS utility, but you can use the windows BIOS flasher provided by your mobo manufacturer too. It's probably better if you do it off a cold boot though. Don't play computer games for a few hours, mess around in Photoshop, browse the web and THEN decide to flash or you'll likely regret it (it might go through fine, but why take the extra risk?). Also it might be best to clock down to default speeds before doing it, even if your comp is 100% stable (I usually don't, but it never hurts to be safe).
I'd say there's probably a 1% chance of anything going wrong. That rises to 50% if you are stupid or don't know wtf you are doing.