Not really sure what you are meaning but I have a similar set-up. I too have a 128GB SSD on that is my operating system and programs. I have 1 x 1TB hard-drive which is just for Steam and other games and 1 x 1TB hard-drive for music,videos etc.
After installing Windows 7 and installing all the update the first thing I did was move all the MY folders to my storage hard-drive (D): instructions. Doing this means that you do not clutter up your SSD.
If I am installing a game which is not a Steam game I create a folder on the games hard-drive (F) and install the game to it. I will still get an icon on the desktop with which to play the game.
If you could explain a little more of what your problem is as you are a little vague.