The easiest way to do a cloning would be like this:
1. Main bay in laptop has a HDD/SSD. Install your other drive into the optical bay spot. Have a third drive as an external with the time machine backup on it already.
2. Hold alt during bootup and select the restore partition
3. restore time machine backup from external drive to the drive you want as the boot drive
4. reboot
5. select the new drive as the default boot drive in system preferences
6. clear off the hard drive, now that the SSD is the new boot drive