I have never had a problem with any method. But, OTOH, no need to go out and buy a USB stick if you don't have one handy. Using the Auto update utility from Windows, click Update, select the BIOS you want and it does everything automatically from there.
Also, When using Asus Flashback and, i expect, various other vendors utility, you do have to rename the BIOS files for it to be recognized ... see step 3 on link below
http://event.asus.com/2012/mb/USB_BIOS_Flashback_GUIDE/