Right click on My Computer and go to Properies. Then go to the Advanced tab > Startup and Recovery. Make sure that Windows 2000 is the default Operating System and then uncheck "Display List of Operation systems for ____ secs."
Restart the computer and make sure that it boots right into Windows2k. If it does, then just delete the Windows folder or wherever you've got Windows 98 installed.
There might be another way, but this worked the best for me.