The first time a score is connected to the Reader, it'll display the Part Chooser.
This is where you select which part you wish to view with the Reader.
The Reader will remember this choice between scores. If you choose to view the Flute part for one score, the next time a score is connected, it'll skip this Part Chooser step and just show you the flute pat already (chances are... you play the flute!)
However, if it can't find a suitable part for you, it'll display the Part Chooser again.
You can switch between Parts at any time by tapping the instrument name in the centre of the toolbar, at the top of the screen. This brings up the Part Chooser, and lets you choose a different part.