When you find skulls, they give you armor and achievements. But you can also activate them to make the game more fun and more challenging. In order for you to be able to activate them you need to go to either the campaign menu or the co-op menu. When you're in there press x on you controller which will make you go into a new menu. This will show you the skulls that you have discovered and a brief description of what they do.* If you click on any of them you will activate them. Also in this menu, you can put scoring on. By putting scoring on, you are able to get some achievements for your gamer-score.
* most of the descriptions don't explain what they do.