First thing is know that all your applications that are installed won't work when you are done unless you reinstall them, and even then it might now work. Also, before you go deltree the WinME be sure to back-up any info saved in there...favorites, email, custom backgrounds, etc...an alternative is to rename that directory to something like 'WinME' and then going into it and renaming the win.com to win.old so that Win98SE won't see it as an OS. Here's what it would look like...I think 😀
REN C:\WINDOWS C:\WINME
CD WINME
REN WIN.COM WIN.OLD
Then you should be able to install your OS of choice...this way if you remember that you need something from your old WinME dir you can just go in and grab it.