if you're installing w2k after winme the only thing you can screw up is to format the c: partition using NTFS. other than that, you can't screw it up.
if you want to use NTFS, install w2k on another partition (formatted at install to NTFS) and w2k will be able to read the FAT32 c: partition.
if you have one partition you can install w2k into another folder on the same drive as winme. this can be buggy and isn't the best solution, but i'm doing that now and it works fine for me. the only thing that has to be done is to upgrade DCOM from www.microsoft.com on the winme to get windows media player and some other software to work. all the software will have to be reinstalled on the w2k. but now i can dual boot winme and w2k and have them both on the same partition.