The easiest, safest way to install the Operating System is to a single hard drive, on a single partition.

Basic steps:
  1. Power down.

  2. Remove the old (working) hard drive.

  3. Attach the new hard drive.

  4. Boot from your Operating System CD and follow the on-screen instructions.
Once you have it up and running, re-attach your old hard drive as a slave (or via USB) and drag your Documents (and whatever else) across to your new hard drive.

Note that at any time you could re-attach your old hard drive and boot your old system up.