As far as program folders:
If you moved the program folder to a different drive, some would work and most would not. For guaranteed operation you would need to uninstall it and then reinstall and select the HDD for the program. In reality though doing this takes away half the benefit of an SSD drive, which is faster boot and loading of programs.
As far as user folder:
In the libraries you can set your pictures, music, documents, and video libraries to be in a different location then the windows drive. This is easiest and more preferred.
You can edit the registry to do a complete move of the user folder including all of the app data. This method has the largest chance of error and will only net you an extra gigabyte of data (mostly...