Yes. Windows would be installed on 1 of your Hard Drives. Then, when you go to install any application, theres usually a "Custom" or "Advanced" button during setup you can click.. this will then give you the option of where you want to save it...
By Default this location would be something like: C:\Program Files\My Program
You would change this to: D:\Program Files\My Program
*Where "D" is the letter of the drive. "Program Files" syntax optional.