I saw quite a few questions on this forum and on stackoverflow regarding ember.js and jQM. It seems to be a common question and since we’ve been using them both since 0.8, I wrote a post with some tips and a working example on how to combine ember.js with jQuery Mobile here:
It includes a minimal example on jsfiddle. The main issues are handling navigation (both ember and jQM have their own confliciting navigation styles) and making jQM redesign an element after ember creates/alters it.
There is a full-fledged real world multi-page application here, altough its much more complicated:
Let me know if you have any questions.