The CMOS memory is where the BIOS stores its settings. Clearing the CMOS memory sets all the CMOS memory locations to FFH this is detected by the BIOS which then loads its default values. Clearing the CMOS does not affect the BIOS program in any way. You should always clear the CMOS after you upgrade the BIOS as the updated BIOS can use different memory locations in the CMOS memory and the different (wrong) data can cause unpredictable operation or even no operation at all.