First, ensure you have the proper firmware for your MB don't forget to consider MB revisions.
Second, ensure you have the proper program for your MB.
Third, either use a floppy or a CD-ROM to place your firmware and writer software on so you can run it from a DOS environment.
If you have a CD-ROM burner: Get a re-writable disk and create a "bootable" CD-ROM. Make sure you include all files required. To learn how to do this from a reputable source (I've used his tutorials) check out:
As far as the MB revision goes, I just mean sometimes various MB revisions require specific firmware, so make sure the firmware you have is for your specific MB revision.
No the .bin file is the firmware/BIOS image that will be written to the CMOS EPROM chip. Usually there is a Program that writes the .bin file to the chip, which can be downloaded from your MB manufacturers site. If they offer a DOS based program for that purpose make sure you include it on the DVD.
Some newer MB's have the writing software built into the MB itself which you access via a specific key press during boot-up. Personally I don't trust those types of BIOS writing programs, but if that's your only choice, check to see if it can read the BIOS.bin file from your CD/DVD-ROM drive. If so that's all you'll have to burn to the disc.
Also if you use some other method than the one outlined at that NU2 site make sure you have the burning software verify the data after the burn. You don't want to write a corrupted .bin file to your EPROM. That will require either buying a new chip or sending in your MB.
One more thing, it's best to have you Computer on an UPS prior to writing a new BIOS. If the AC power is interrupted during the BIOS write, well see the last sentence of the previous paragraph.