You will need to reinstall the programs anyway, so I would take this opporunity to correctly install them on the same C; drive as OS.
You can keep your data files on the separate drive to see if they are correctly referenced by the programs, linking them to correct User folders by the method in User Folders - Change Default Location
tutorial, or by rightclicking on file/folder to include in the relevant library.
In Windows 7, Documents for example is a User folder which can be placed on the drive you want using tutorial, and is also a Library which can include any file/folder simply by rightclicking to Add to Library.
This will become more evident after you reinstall and setup. But you will not be able to keep programs already on the separate HD as programs always need to be reinstalled.