Your programs will have to be re-installed to reference your new boot drive appropriately.
A fresh install of the OS to the SSD would be best in your situation. But if you don't want to re-install the OS, you can uninstall your apps and then clone your HDD to your SSD, boot to your SSD and then re-install your apps to your HDD.
Hindsight being 20/20, I've found it's always easiest to upgrade your boot drive if you don't put any apps on it. I just put my OS and drivers on one SSD. That way, if a new SATA spec comes along (ie SATA IV), I can just clone my OS/driver drive and everything else stays in its place. Apps are on separate HDD or SSD drives and data on other drives.