Does anyone know if the parts are transposed for the different instruments or are they all in concert key?
Adam if I understand your question correctly you want to know if Noteworthy automatically displays an Eb Alto Sax part, for example, with the correct key signature relative to concert key for that instrument. No, but what you can do is notate every part in concert key to start, then use the Transpose feature. Highlight the staff you want to transpose, then choose Tools, Transpose Staff.
The score should be written as a transposed score.
That way the notes on the parts can be checked directly with the conductors score.
A concert score could be used but to avoid confusion with transpositions between the score and parts a transposed score is preferred.
Both transposed and untransposed come in handy. The problem with a transposed score is that if there's a mistake in one instrumental line, it's a little more difficult for the conductor to recognize the chord.