dwujcikIs there a particular reason you need to update the BIOS by script?
Updating the BIOS is a risky business, I've seen many a motherboard reduced to a useless lump of plastic from a bad flash (bad source, power interruption, flawed stick of RAM, etc).
My gut reaction to your question is "OMG DON'T DO IT!". If you're not at the site with a replacement board handy, don't do the update. If you accidentally push the wrong update, you could brick every machine that runs your script.
I've also found that updating from within Windows has a fairly high failure rate. Do it from the BIOS itself if supported (sorry, last I checked Intel doesn't offer this), or from a boot "floppy" (rig up a flash drive or CD for it). There's really no way to automate this (not easily anyway).
I spent a few years in computer repair, and done BIOS updates as POLICY on new motherboard sales. Every now and then the board has to be replaced after a BIOS update, even though that image worked on the board before it, and the replacement.
BIOS updates are usually only needed to add support for a specific CPU (the only reason we did the update there). Sometimes they fix glitches or add functionality, but that's rare. If you're doing it to trouble-shoot a machine, it looks better if you're at the machine when it bricks than if you come running in the day after an entire network croaked with a pallet full of new motherboards...
There's this one ASUS BIOS update for the P5N32-E, that's meant to fix a specific problem with high-end video cards. I had to buy a new motherboard after applying that update, and yes, everything went perfectly.
If the machine is working fine, don't update the BIOS.
Having said that, just wrap the command you need in a .vbs (or a .bat) and push it alongside the update, and call the .vbs (or .bat) from your script. Add ">> output.txt" to the end and you'll get a txt file with all the screen output for you to review after. Substitute the name with whatever you want. Set the script to e-mail you the contents of the file if you want. The update might require user intervention, in this case there's some automation programs you can use, or you could even expand a .vbs script to click on those buttons for you.
But again, NOT recommended. Automatic BIOS updating is like playing with with a rusty propane tank next to a bonfire.