In most cases, the latest BIOS update is cumulative, with all of the past fixes, additions, changes that were provided by the previous BIOS, in addition to whatever the new BIOS has. I've flashed boards with the first rev of their BIOS to the latest and never had problems, providing that the latest BIOS does not call for a specific revision of the board. If that is the case, the manufacturer will usually point that out in the release notes or on the webpages for the updates.
I have always used the bootable floppy disk approach, as this almost never fails. Get a couple of floppys, do a Full format on them to make sure there are no problems (bad sectors, etc.) and make one a bootable Win98 disk and but the update files on the other diskette. Its fairly foolproof this way, as long as you follow the instructions on flashing from the manufacturer.
Hope this helps and good luck
Matt