Instead of trying to figure out how jQuery + underscore + backbone + jQuery UI all work together, or shoving your jQuery code into EmberJS, take a look at YUI (http://yuilibrary.com).
The framework is very well built, it's entirely modularized, and it has support for JS app infrastrucute as well as modules like Autocomplete and Uploaders. Bonus: the gallery is full of well written useful modules you can plug and play.
It's not just used on Yahoo!'s high traffic websites, it's also used by Zillow.com and other large scale websites that have complex JS needs. The code is easy to modularize and the whole system can be versioned for incremental upgrades.
Some additional helpful resources: