If you're using an older version of Partition Magic, like 4.0 I believe, you will have problems (NTFS).
Current Versions, like 6.0 or 7.? work just fine with Windows 2000 and NTFS.
If you're just trying to format and partion a new drive, Windows 2000 Professional "Disk Administrator" can do this just fine. But if you have an existing HD and want to change/resize partitions you will need a 3rd party software program like Partition Magic.
Good Luck!