Is the PC that you are putting this hard drive into afte rthe OS installed exactly the same as the PC you are building it in? If not expect huge issues =)
Other wise...couple things to do.
1 way would be diable the HDD in the BIOS that you don't wanna use. So if you are gonna install 2000 on the second HDD disable the 1st one.
2nd way you could try is just install the OS and it will ask you where it should be installed. I think...honestly I have never tried it so couldn't tell ya.
Hope that helps.