If you need to do it on 2000 file format, there is a reference manager for that as well. If you use the 2004/5/6 version, you will migrate all your files up to the new version when you do that.
It will work very well and do what you need, however it might take a little while if you have lots of files. Sometimes the program will hang up if you load in over 100 files at a time. it really doesn't hang up, it just seems like it does. If you just let it think and go get a donut or something it'll be there when you get back.
If you need help ask away as I use it all the time.
Pieter