When you enter a piece, Metronaut chooses the best available score/arrangement best on your selected instrument. If you have selected a transposing instrument (such as Clarinet in A), Metronaut transposes the score so that the Audio and Score match your transposing instrument. Since iOS version 1.9.5, Metronaut also changes the Clef of the score, especially if you attempt to play a score not originally written for your instrument (e.g. you are a Double Bass player attempting to play a piece originally written for Violin).
You can also transpose the score yourself from the score view by dragging the Settings bar at the bottom of the score up : In the transposition tab you will be able to transpose up or down an interval (best for singers), an octave, directly change the scale (best for transposition instrument), or change the main Clef.
When using a transposing instrument (for example Saxophone Alto in Eb) on a piece in a different key (for example in C), Metronaut will actually transpose the Accompaniment Audio and leaving the music score visually intact but in your preferred key.