If you have a full win98 CD, Start with Start disc click here change to your CD Drive Letter this will more than likely be one letter different, if it was D:\ it will be E:\ then type setup and press enter
The Floppy must be a "Setup disk" because this will have the DOS drivers on it which you need to access the CD. A Startup flopy will not (usually) do this for you.
I have not done it this way, but I am told that if you get into the BIOS (usually press delete during early boot-up)then set the first boot device to be CDROM, (you scroll through the options using Page Up or Down) - your computer will find the Win98 CD and you can type setup from there.
When installation is complete as far as basic Windows, you must go back to your BIOS and reset it to HD drive 0 or Floppy for first boot device,