That (new) software should have all the instructions for it. Normally you install the new HD as slave, do your transfer-stuff, then switch off, swap the HDs and set old-master to slave and set the new-slave to master. When you reboot, check in the BIOS that HD-detection is set to automatic for both drives, or use the HD-detection part of the BIOS first. Then you can wipe the "old" HD that is now slave, if everything works to your liking.