If you are referring to the utilities, I can only speak for my model of board (Asus A8V). The preferred one, according to the website, was the afudos. But, I had problems with that and I ended up using QFlash, which is already built into my board. I can't remember the exact sequence, but it required holding a couple of keyboard buttons during the boot, and once Qflash began, it was self explainatory and easy. As for me, I would never use a utility designed to work while in Windows, because if their is a BSOD or anything goes wrong, you've fried the bios, and would have to send it to Asus for repairs that you would have to pay for. Oh yes, and with that particular utility you have to rename the bios download to correspond with the model of the motherboard.
EDIT: I may be wrong about the name of that utility, because that is the name of a Gigabyte Flash. I'm not sure, it may have been Easy Flash. I would try to look it up, but when I tried to go to Asus earlier, none of my browsers could get there.