When you boot of the windows 2000 disk it will ask you what partition you want to install to, then it will give you a couple options including deleting the current partition by pressing D, which you should do, then make a new partition then select to install to it.
4 some reason i put the CD in, and it says that a file is corupt or something? i tryed it 2 other times and still the same thing, maybe i'll just put that drive as a Slave, and format it that way.