You can also update from within the bios - alt something or other (look in the manual) to avoid even booting into DOS.
However, folks say that if you do it from the Asus BIOS utility, it does not zero out the BIOS RAM, it just writes over it. I have done it both ways, and from the BIOS the progress bar shows a darker color that just gets overwritten. When I have done it by booting from a USB key, the DOS proggy shows an empty line that fills up. Who knows for sure?
I now stick with the prevailing wisdom - do it from DOS. I have seen BIOSes do funny things, lock up, and act strangely from time to time, but DOS is always smooth as silk.
Really don't do it from Windows. A hard drive burp, your anti-virus deciding to do a scan, a sudden glitch from the onboard sound, anything could screw it up. Why take the chance? In DOS, only a loss of power or floppy/USB failure could screw things up.