There are three basic ways you can attack this.
1. Reformat and start from scratch. In my opinion, by far the better way, as it eliminates potential conflicts, but the downside is, you will loose everything on that Partition or Drive, and so the requirement to backup everything you need is most important.
2. Make a floppy start-up disc, boot from it, and let ME install as an upgrade to '98. This will work, but almost always leaves behind remnants of files, that not only clog up the system unnecessarily, but can cause conflicts.
3. Set your BIOS to boot from the CD as First boot device, and continue as 2.