What is BIOS? It is an abbreviation short for Basic Input Output System also referred to as the CMOS. It is what tells the computer parts how they can relate with each other. To store the settings, the BIOS relies on a motherboard battery to hold onto the setting changes you make.
On computer startup, the information you see is from the CMOS. After it tells all the components how they can relate to each other, Windows boots, using the settings provided by the CMOS.
When it comes to setting up the CMOS the best time to play and learn what the settings do is after you have just built a computer, or before installing or reinstalling your operating system. This way if you change any settings that effect your operating system, like accidentally deleting a raid configuration, you have nothing to lose.
The CMOS is upgradeable, it may add features or additional support for new CPU's. I would not recommend flashing or upgrading unless there is something you specifically need, or really want. This is a risky process and the potential to have a damaged motherboard can result.
If you have determined that you need to flash your CMOS for any reason, this is what you need to do. Make sure you have stable power, no storms rolling in. A disruption in power will be a problem. Follow the exact instructions given by the motherboard manufacturer on their website. Different motherboards flash differently.
My most recent CMOS upgrade was done on a Gigabyte motherboard in Windows. This was the best experience I've had so far. I liked the Windows process much better than doing it from DOS.