I have done this several times - the first time I did a transfer with the DVD provided by the drive. Performance wasn't 100%, and eventually I removed the hard drives and reinstalled Windows 7 on the computer with only the SSD installed. Performance increased dramatically.
After the installation and updates, I placed the two drives back in and made sure to boot from the SSD. I copied files from one drive to the second, formatted the first, and moved all data to the first drive, and then formatted the 2nd drive. Then I setup my regular backup routine.
My initial setup was one OS/Data drive and one backup drive.
On my wife's PC, I backed up her data, removed the HDD, installed the SSD & installed Windows, then added the drive, formatted and restored her files. Top performance from the beginning.
The "transfer" method with their migration software is good, but you won't be at 100% efficiency without installing Windows on the SSD when only the SSD is present.