The small SSD is much faster than the large spinning drive, so you should install most applications on the C drive for performance reasons, although perhaps not very large applications such as games since that would probably cause you to run out of space on C.  Your "bulk data" such as photos, music, videos, etc., as well as applications that are large and/or where performance isn't a major issue should all be placed on D.  For applications, this will involve manually changing the default install directory from C:\Program Files to D:\Program Files, for example.  For your other data, you can manually create whatever folders you want and organize your data however you want, and/or if you want to formally move your Libraries folders such as Documents, Pictures, Videos, etc., if you right-click each of them and select Properties, you'll see a Location tab.  When you click that, you can choose where that folder actually resides on your system, so you can change it to your D drive if you prefer.