CMOS is basically 'BIOS RAM' and is powered by a battery on the MoBo, so even when the system is off, it retains it's data. The data it stores is the BIOS settings (data/time, hardware configuration, shutdown temps, etc.). Basically, when you start your system, it will POST, during which CMOS is 'read' and the system looks for everything that CMOS says should be there.
During some hardware changes, you need to clear the CMOS data to allow for updated data to be stored. Since CMOS is battery-powered, you can't clear it by cutting power - you need to set the CMOS jumper to the 'clear data' setting. The jumper area is comprised of three pins. Usually the jumper is set to pins 2 and 3 to allow for normal use. When clearing CMOS, you would set the jumper to pins 1 and 2 for a period of time (usually 10 seconds, never more than 30 seconds). By doing this, you are telling CMOS to erase itself. After it's cleared, you set the jumper back to the original pins and and turn the system on.
Now, your system will POST as normal, but not find CMOS, so it will flash a message that you need to enter BIOS and set it up. You can spend as much time or as little time doing so as you want. All you must set are the current date/time, after that you can adjust individual settings, or go to the 'Load Optimal Defaults' (or similar) and factory-settings will be loaded. Save the changes, and the new data will be written to CMOS. System will reboot, and this time POST will see the new data and the system will load.
Edit: Sorry for not mentioning before, but if you didn't know, POST stands for Power-On Self-Test, and it...well, tests the system when started!
