I've been wondering about the same thing.
You can print out {{controller}} in your template to see the name. If it's generated it will say something like "generated controller xyz". If your custom one is picked up it will print that out.
It would be great however to include some debugging tools since sometimes you can even wonder how to name your templates.
An area that has caught me out many times has been when my naming hasn't quite matched the conventions. Because ember provides default implementations at runtime you don't know if your implementation has actually been picked up. Is there any way to enable some logging output that would show whether the default or custom implementation is being used? If not this would be a great addition to the development experience.