I have a complex iPad view that I manage by having several view controllers. I previously (before iOS6/XCode 4.5) did this by allocating my view controllers in code, and hooked
I'm not sure what you mean by "retrieve the embedded controller". When you want to use a controller you use the UIStoryboard method instantiateViewControllerWithIdentifier:, using the identifier that you give to the controller in IB. You can also use the performSegueWithIdentifier:sender: method (which also instantiated the view controller). You should check out the "Using View Controllers in Your App" section in the Apple docs. It also makes reference to the fact that child view controllers are instantiated at the same time as the container controller.
After edit: If you embed a container view in another view controller, that embedded view's controller can be referenced from the containing controller with self.childViewControllers (which will be an array, so if there is just one, you can get it with lastObject).