Ember doesn't really hijack your JS folder. Simply put the code inside an "ember" folder to separate it from your own JS or other libraries you're using.
It should then look something like this (unsure about some of the ember files):
+ app
+ assets
+ javascripts
+ ember
+ components
+ controllers
+ helpers
+ mixins
+ models
+ routes
+ templates
+ components
+ views
- app.js
- router.js
- store.js
+ jsmd5
md5.js
- application.js
Your application.js might look something like this:
# for more details see: http://emberjs.com/guides/application/
window.App = Ember.Application.create()
@import "jsmd5/md5.js"