Most MOBOs take a pretty standard button cell battery and changing it is just a case of popping one out and clipping the replacement in, usually a CR2032 or CR2016 I think, but do check it first as there are variations on a theme.
Its been that long since I had to replace a CMOS battery I really can't remember. I think it does lose the setting but I have all mine written down in the back of my manual anyway.
Boots the Chemists sells them as do many other places, don't let a PC shop charge you a fiver for it saying its a specialist item cos its not. Many places will have them they are used in watches, hearing aids, calculators etc. Get the same number though.
Your Bios update will be OK. It wont need flashing. Once done that's how it stays, but like the earlier version it will default to the factory settings.
In my limited experience there are very few changes made to BIOS settings by most people. Usually a matter of convenience rather than life or death choices. As others have said boot order is a favourite one and easily corrected to what you want later.