In order to use the Windows 98 Second Edition Boot disk file, you need to do the following :

With your computer booted up and running , go to Start > Run  > Type in Command , then click on Open.

Put a Blank Floppy disk into the A: Drive , at the prompt type in Format a: /s    , then press Enter.

After this gets finished, download the zip file and unzip it to a destination of you choice , 
afterwards copy the contents of the destination folder to a: .  You now have a Win98 SE Boot disk .