Magikal,
Open a command prompt. Type "convert /?" (no quotes), then hit the Enter key. The little list of information there will tell you how to convert any FAT or FAT32 drive on your system to NTFS. You should be aware that this will cause your cluster sizes on the converted partitions to be 512 bytes in size. That is SMALL. The only real problem with that, unless a given partition is really huge, is that the small cluster size will lead to MFT fragmentation, and that will lead to very poor performance. You can prevent that from being a problem by getting a third party defragger which is capable of doing boot-time defragmentation of the Master File Table, pagefiles and other specified files.
When you say that you upgraded, do you mean that you installed Windows 2000 on top of some other Windows OS? If so, and if you're seeing very slow performance from your system, I'd suggest that the slow performance may be the fault of the install-over. A clean installation results in a much more efficient system.
In any case, whether you convert or format / install, save your data to external media before proceeding so that you won't lose it if something goes awry. And, if you install W2K clean, you can specify a cluster size when you choose the file system type. Most people seem to think the 4,096 bytes is the optimum cluster size for a personal user of W2K.
Hope this helps.
Regards,
Jim