yes you do with aps and games there needs to be bits of the installed games placed into the registry of the windows os.
when you do install your games and aps back if you dont want them on the ssd you have to do a custom install and tell the installer to place the game or program on the data drive.
You need to re-install all the programs. There are some exceptions, for example I can copy the World Of Warcraft folder from Program Files from one computer to another and can start the game without actually running the setup for it.
When you install new programs, as the post above ^, you can often change the setup directory (you can probably just change the C:\ to D:\, although you will still have some info on the main Windows drive.