For the programs to work they need to be installed on the Drive with the OS.
Now if you have one Drive with the OS and programs and a separate Drive with all your stored music, videos, documents etc etc. Then you will see a slight increase in Boot times as well as file access.
That's what I did. My OS, games, and programs are on my primary while all of my music, movies, documents, ect. are on my slave and it works wonderfully.