To install Windows 98 you always use a floppy to boot. If the system has to be repaired, do it from the floppy.
The OP is probably long gone, but a floppy isn't necessary to boot Windows98 SE, it's a bootable disc. It was only necessary for pre-SE versions of 98 and computers that didn't support booting from a CD, which I'm guessing this one does since they were able to set it in the BIOS.