Wrapping my head around Ember App Kit -differences compared to working with plain Ember

I have begun using ember app kit and heave read through its guides. However I having trouble wrapping my head around the differences between a regular app and this way that Ember App Kit structures the various bits using ES6 modules instead of stuffing everything into a global variable used as a namespace (e.g. App).

I found that this aspect is not very clearly explained:

• How does Ember apply its magic in auto generating models, views, routes, and controllers?
• Where does it expect to find them?
• What naming conventions should I follow?
• If I have created a template, route,or controller, and Ember does not find/ detect it, and just generates a default one in its place, how do I find out where it is looking; or otherwise debug in this situation?
• How is any of this different in the standard Ember app development, as compared to development using Ember App Kit?

Much appreciated in advance!

EDIT (20140506):

These resources explain ES6 modules and EAK really well:

• A brief overview: eviltrout: getting started with ES6
• An entire series of posts: [toranb: http://toranbillups.com/blog/archive/2014/04/06/Building-your-own-ember-app-kit-lite/), with an ES6 modules specific one

I actually did a blog series on this very topic just a few weeks ago. I start with a basic (globals) ember app and transform it over 8 different posts.

• Part 1 - Introduction
• Part 2 - Concatenation (introducing Grunt)
• Part 3 - Handlebars template precompilation
• Part 4 - ES6 modules
• Part 5 - JSHint
• Part 6 - Watch + Live Reload
• Part 7 - Testem
• Part 8 - Deployment

In the end, you have a Gruntfile w/ tasks just like EAK (but you've built it all by hand -one step at a time)