Yes, you can use a bootable cd to update the bios. Just make a bootable cd using nero or easy cd creator, you can use floppy emulation or load an img.
you can find img files for bootable cd's by searching on google, most of them make a win 98 boot disk.
Just add the bios updater to the cd and your off and going. When it gets to the command prompt, type the name of the executable and hit enter, follow the steps and your bios is updated.