After creating the new partition and installing, make sure you choose a New/Fresh Install (not the upgrade!). You'll also want to make sure to check the box so that the install will prompt you to choose a partition during the install.
For most programs, especially ones with variants for Win2K, or registry entries, you will need to reinstall them under Win2K to get it to run. Doing so really sucks up a lot of room. So when I did it, I knew I was going to use Win2K more than WinME, so I installed WinME and almost no programs under it and then installed Win2K and all my programs under that os.
You'll need to install drivers for all the hardware, make sure you use the Win2K versions and not the WinME versions.