Make sure you have;
1. Windows CD & Serial Key
2. Hardware drivers
3. Bootdisk - this can be created by windows, or bare minimum; put a disk in the floppy drive and type "sys a:". this copies boot files and a command interpretor. Then find "format.exe" or it might be "format.com" and put that on the disk. Find your CDRom driver. With windows98, there is a file called "oakcdrom.sys". Put that on the disk. Also copy a file called "MSCDEX.exe". Open edit and type the following;
And save on the floppy as "Autoexec.bat". Open a new file and type;
Save that file as "config.sys". Put the disk in the drive and boot. You should have a command prompt and be able to go to your CD Drive by typing say "D:". (the drive letter will be revealed for the CDRom when it laods the drive, so read the screen). If you can read the CDRom by typing "dir" you are laughing.
Now to format, go back to the a: and type "format C: /s". This will cleard the drive, reformat and allow it to boot. Then reboot and go to the CDRom and type "Setup". You should be prompted on what to do.
I think all of the above is correct, but I am doing it from memory and reinstallations often go wrong.