I've always downloaded the bios files and saved them on my computer, then used the "update bios from file" option in Asus Update. Works fine, it will not fry your board.
I,m currently using the 1011.002 beta, and I have tried every beta and released bios thats been issued (20+) using this method with not a single problem
Just make sure you download the latest version of Asus update V6.05.01 if you use bios 1007 or higher
2. I've never gotten Cool n Quiet to work? Although I only tried it once very quickly. Asusprobe works up through bios 1007, for 1008 and higher you have to search for and download Asusprobe II (much better than the original)
3 For the nvidia drivers, you go to the nvidia website and download the Nforce4 standalone driver kit. And you just install them, no need to uninstall the old drivers.
The lastest released one is 6.53, there is also a beta (dont remember the ver.)
*edit* I can see you feel comfortable with the Autoupdate method, IMO it is the riskiest method of updating the bios. I would rank the methods from safest to riskiest
1. In DOS using a floppy
2. Asus Update from file
3. Asus Update (Auto update)
The Auto update is essentially the same thing as the update from file, except the file is coming over your internet connection, so if theres a glich in you connection or you lose connection while updating the bios WHAMO! It adds an extra layer of risk. But it is by far the easiest method. I use the #2 method because its safer than #3 and I'm too lazy for #1
#1 is always the safest. Download the AWDFlash utility from the Asus website. Save it and the DOS version of the bios that you want on floppy. Boot up to the floppy and follow the instructions in the text file that comes with AWDFlash