Just as c0re said, the C: partition is for system files like your Windows and Program Files directories. D: partition is used for your own personal files. This way if you ever wish to change your operating system, your personal files are stored on a separate partition so they won't be affected. Your 'My Documents' or your documents library (depending on which OS you're using) should be set up to be stored on your D: partition. If it isn't you can set this up yourself and this is probably a good idea Google is your friend, just bear in mind its different on each operating system Hope this helps!
Its good to have a small C drive, put games and other softwares in D drive, by default your computer will always seleect C, you can always select any other drives to install softwares or store data files.
The reason for the small C drive is incase Of Virus attack or system crashes warranting reinstalling of Operating System it might be possible to save important data on other drives while only deleting data on C drive. You can always use short cuts on desktop screen while keeping the main files in D drive.