Alloc init'ing cvc is not the right way to get your reference -- that's a new instance, not the same instance as the one embedded in your view. You can access that instance in code from the parent controller with self.childViewControllers[0] (assuming you have only one container view). You can also get the reference by implementing prepareForSegue and use segue.destinationController (that will be your embedded controller).
What you seem to be missing in your understanding, is that the controller you get when you use a container view in the storyboard is a child view controller. It's the same as if you had called [self addChildViewController:whatever] in code and then added the child's view as a subview of your view.