If you're starting the installation by booting from win2k install CD it should ask for a qualifying CD (eg, win 95/98) during the install process. If you start from within 98, it should be ok as you obviously have a qualifying product.
So which did you do - and where did it stop?
PS. It is much better idea to do a clean install (you can do this with upgrade disk - see scenario 1 above), after backing up you data. The upgrade route just sets you up for likely problems in the future.