When using an audio interface with multiple outputs, and need to turn the click on/off or turn the volume of a click down on a track, you want to change these settings within the "Output" tab of the Mixer inside of Studio One 2 (Mix can be located at the bottom Right corner of a New Song or template, or by pressing F3 on your keyboard).
As depicted, click on the Outputs tab >> Then find the output (based on the white area below the fader you created in Song Setup), and click the Metronome below the output designated.
NOTE: The output metronome is for that output fader only. Turning these setting off on the output does not turn the metronome for the Main output off. It is only for the selected fader and is post fader from the physical volume fader position.