If You are using Phoenix 1.3.0-rc, You will generate a structure like this
- my_app_umbrella
- apps
- my_app
- my_app_web
- apps
where my_app will contains db layer, and web as the interface.
I do not see why You are using 3 phoenix apps, 2 without servers, because You could simply create Elixir project with mix new, that should be enough to decouple backoffice/frontoffice code.
And now You would put guardian in the my_app_web.
Maybe You don’t use the same version, or maybe You really need 3 Phoenix apps. So maybe my post is out of topic.
But that would be the way I’ll go with your description.