You can chose to display the score in either written or concert (sounding) pitch. Written pitch displays the score as it should look when printed for musicians to read. However, during preparation you may prefer the convenience of seeing the transposing instruments notated as they sound, without transposition. In this case you should select the "Concert pitch" option.
To toggle the score display between written or concert pitch:
Before printing the score, exporting it to PDF or saving it online, you should ensure that the Concert Pitch button is off, and that the individual parts are correctly transposed.