So I download the software to my old harddrive, then I boot the secondary hard drive first? Can you please list the steps of what I'm suppose to do.
It depends on the new HDD you purchased. You use their cloning software and usually done from a CD so you can clone bit by bit your OS partition to your new HDD.
Since you haven't shared your computer specs, old HDD and new HDD, it's just generic info. Follow the manufacturer's instructions. You can also use Acronis True Image or Norton Ghost, separate programs that will generically clone one HDD partition to another.