I’m not 100% sure I get everything you’re after—are you saying the schemas would also live in the library? If so, off the top of my head I would:
a) I would create a custom mix task in the library that will generate the appropriate migrations into your app.
b) Add a config option to your library to set the Repo it uses: config :my_library, :repo, MyApp.Repo.
In terms of keeping schemas in a library, I could see you running into problems where you’d want associations from your app on the schemas in your library, maybe. You could possibly run into some other issues too 
But anyway, this is one way to do it!
