You can create your additional views inside a storyboard if you prefer. The key is to create them in the same ViewController Scene, but outside of the viewController. Create an IBOutlet for the view in your viewController.m by dragging the secondary view to the viewController and then you can access it in the same way you would with any other IBOutlet. If this is a custom view you can set the class in the identity inspector as you would with any other custom class in storyboards.
For a full example, look at Apples KeyboardAccessory sample Code, specifically, look at the AccessoryView