TuneUp has traditionally "attached" to the right side of iTunes, allowing users a useful and convenient way to use TuneUp as an iTunes companion application. The Mac App Store version of TuneUp offers a choice for users, and you now have the ability to run TuneUp either attached to the right side of iTunes or detached and running as its own window.
When you launch TuneUp for the first time, it will be "Detached". If you wish to attach TuneUp to iTunes at this point, you simply need to click on the Attach Icon at the bottom of TuneUp - - do the reverse and click the Detach Icon if you wish to Detach from iTunes.
Attach and Detach are also available within the Window Menu of the OSX Menu Bar.
While TuneUp is Attached, it will respond to many window and application commands that you apply to iTunes, such as the Close, Minimize and Zoom buttons in the Title Bar: