Program all blocks, destroy CMOS checksum. This will ensure no traces of the old BIOS that might cause issues will be left over.
No don't flash all blocks! Like Yen said, if you brick the BBL you greatly decrease your chances of bios recovery.
In general dont flash from within WIndows at all! Simple as that. Afudos will leave the boot block as is using standard option /i<biosname.rom> (without brackets) if you have allready flashed with same revision bios before. So flash the original unmodded bios first (also from dos) then flash the modded version and afudos leaves the boot block.
+1 Flashing from Windows is more susceptible to failure due to other running processes than by using DOS (i.e. Boot to pure DOS, not just a CMD prompt). There are occasions where re-writing the boot block may be necessary, but leaving the BB alone means you have a much better chance of recovery if there is a problem due to a failed flash. Only update the BB if the manuf. specifically requires it for a newer BIOS version.
++1. As a rule I never flash from within the Windows environment, too much background stuff that can interfere (e.g. a background app/service can cause Windows to hang for a brief second...) I have seen too many problems in my day due to the simple fact that someone flashed their BIOS from within windows...