When TuneUp is Detached from iTunes, it will operate just like any window within any Mac OS application. TuneUp will no longer respond to Close, Minimize, and Zoom commands performed on iTunes, but those controls are all available for TuneUp when Detached:

While Detached, you can move TuneUp anywhere on the screen. Addtionally, the "Grabber" becomes active so that you can change the size of TuneUp vertically.  At any time, as long as the iTunes window is visible, you can click the "Attach" icon and TuneUp will move to Attach to iTunes and resize appropriately.