Your question is still a little confusing ...
Boot into the backup BIOS - select the switches to, say, bank 1 (on,on,off,off) and then flash away! the BIOS will go into the banks you have selected.
To update the backup BIOS you need to go into the config live settings - but I wouldnt go there, it's there for a reason and if you frick it up ....
Hope this anwers your Q.
J