First. See if your system can boot from CD. That would make everything easier.
If it can't then do one of the following:
1) Use a bootdisk from
www.bootdisk.com
The site contains instructions on how to get everything working. I never figured out those MS OEM boot disks. They never seemed to work correctly. I just made one manually, but maybe if you haven't used much DOS then it may not be an option.
2) If you're not planning on formatting the hard disk, copy the win98 directory from the cd to somewhere on the hard disk. (i.e. c:\win98)
reboot and press F8 as windows starts loading to give you that little menu thing. Select "safe mode command prompt only"
When you get to the c:\> prompt, type:
and setup should start.