Windows 2000 is installed with the NTFS as default, I don't think you can run it with a FAT32 file system, might be wrong but don't think so.
If you use an update disc version of XP somewhere along the line during the installation you will be given a choice -
'Install Upgrade' - 'recommended'
and beside the choice will be a dropdown menu arrow, when you drop down it, it gives the option to install a clean installation, select this and you will then be given the option to format the existing installation as FAT32 or an NTFS, choose NTFS 'quick' format.