Tim - I really wouldn't bother. I feel that Windows 98 Second Edition is far better than Windows Me. My other thought is that Windows Me is just 98 with an updated look and a couple of extra features. I also don't feel it is as stable as 98SE.
However, if you wish to upgrade using an upgrade disc, all you need to do is boot into Windows 98 as normal, insert the disc and follow the upgrade instructions. It should be pretty straight forward. As it's only an upgrade and not a clean install, you shouldn't face any technical issues.