If you are using Cocos2D for your game, you should probably get in the habit of building your settings screens as Cocos2D scenes or layers, which offers the benefit of easily animating them into and out of the frame during your game. Adding a view controller is not necessary and actually complicates things when it is so easy to just create a CCScene or CCLayer.
I prefer the CCLayer approach, then I can animate the layer swooshing into the frame when a user presses a Settings button. The underlying game play is not erased since it is the same scene.
Another approach is to pop a settings scene onto the current scene.