Hey there, Rayleigh06.
No sure which program you're talking about. It would be wise to get in touch with the developer's customer support and ask for assistance on how to migrate your OS. Most cloning programs should be able to clone separate partitions and not the whole drive so it should be possible in your case as well. Other than that, you can give this tutorial a try: http://lifehacker.com/5837543/how-to-migrate-to-a-solid-state-drive-without-reinstalling-windows. It might prove useful.
Please remember to have a backup of your important data, just to be on the safe side.
Hope that helps. Please let me know if you have any questions.
Boogieman_WD