Hi Dave,
This thread may be of some use to you.
But basically, it’s up to you. Discourse (if you’re not familiar with Discourse, it’s a new, more modern, pro-user experience take on forum software based in Ember - ones of the largest Ember apps currently out there for sure) keep all their public resources in an assets folder, then seperate by js, css, fonts and images. Within the js/discourse folder, you can see how they structure their Ember files.
Hope this helps.