There really is no *safe* way to update the bios... if for some reason the writing of the image to the chip fails, you've bricked your box.
That being said, Asus's utility is probably the safest thing you can use to update your bios image. In addition to their windows utility though, Asus offers on their newer mainboards a way of writing the bios from the early boot environment (i think you hit 'f2' at the post screen).
One thing I will mention is that there is another open-source utility called 'flashrom' that can be used to read & write the chips from quite a few mainboards... I'm not sure if supports newer intel-based boards, but it is quite nice to use if you're comfortable with the Linux command line. I like using it to make a byte-for-byte copy of the bios on boards that i can use it on so i can look at binary diffs