I'm trying to remember a book series (I THINK it was 7 books long) that followed a teen boy in a fantasy world. All I can really remember is that his father was thought to be dead, and in the book people could use the stones to create things (like the Green Lantern). I do remember that they forced some storm cloud beings to serve them and be their shadows.
I believe you are looking for Garth Nix's Seventh Tower series. The Chosen use Sunstones to bind magical creatures to them as Spiritshadows. These Sunstones also function in a manner similar to a Lantern ring in that they can create constructs of light.
The storm cloud beings you mention are Adras and Odris, Storm Shepherds, that the two protagonists encounter in the third book.
The description reminds me of the broken sky series I read a while ago, people receive different coloured stones for different powers early in their life.