I guess you are trying to re-install windows - right? To do that your system needs to able to read from the CD drive before Windows is installed - it can't do that without first booting from a special floppy disk called a Windows 98 Startup Disk (also called a boot disk). This boots the PC into DOS and loads a DOS cd-rom driver to allow the PC to 'see' the Windows 98 setup CD. You might have already made a boot floppy when Windows working, but if you haven't got one you can download one from here: http://www.bootdisk.com/bootdisk.htm
Download "Windows 98 OEM" boot disk. Create the floppy.
Boot from floppy and choose "Start computer with CD-ROM support", then press 'enter'. Put the 98 CD in the drive, and at the prompt, change to the letter used by the cd-drive (it will be 'E:' or 'F:' depending on how many hard disks are fitted).
Then type SETUP and press enter.