I take it that you have a good start up floppy for 98-se, that includes CD rom support. Set your bios to boot from floppy first. Then boot the PC from the floppy, (choosing boot with CD rom support), and you will find that your CD drive will have moved one letter down. If it was D is should now be E.
If you have 2 CD dives, say a burner and a normal reader, then you may find that you will have to discover which of these drives is being read, as both will not be. I assume that you have already formatted your hard drive, if not, do this now. Having done this, insert the Windows CD, and type E:setup (assuming E is the CD drive), if not, try F:setup
This should start the installation procedure. I am assuming that you do not have any partitions on you hard drive and will not need to F-disc.