It depends on what you install. Most programs has the option to select what drive/directory upon installation. Pero yung registry and some data are placed in system drive which is drive c. If it is an important program (example a driver update like nvidia drivers) then let it install in the system drive, if not then drive D. You can install games in drive D without problems.
Use ccleaner too to clean your drives, and move large files like movies,videos, music etc.