I read the following instructions on another forum and thought they made the most sense, assuming it works as described:
Upon arrival, boot up the system, do the initial OS setup, launch AlienRespawn and create the recovery media.
Swap in the new HDD/SSD, boot up with the recovery media and follow the prompts to restore your factory image.
Poof, all done - aftermarket drive is in and you can setup your system and go from there.
That recovery media is very handy. Make sure you create it and stash it away for a rainy troublesome day.