The Output Volume is set with the Fader on the "Output Channel Strip". This is the bus you route all your Channel Strips to (Audio Channel Strips, Instrument Channel Strips, Aux Channel Strip). Logic creates a dedicated Output Channel Strip for each output on your selected audio interface (mono and stereo pairs).
The Master Volume is set with the Fader of the Master Channel Strip. If you are familiar with the concept of a VCA Master Fader, that's what it is. That means, you just set a dB offset to the level of your Output Channel Strip. The Master Channel Strip has more functions when working in Surround. In stereo mixes, just make sure that it is always set to 0dB (Unity Gain), which means, you can ignore it.
Here is a diagram from my book "Logic Pro X - How it Works", where I explain the concept in more detail

Hope that helps
Edgar Rothermich - LogicProGEM.com
(Author of the "Graphically Enhanced Manuals")
http://DingDingMusic.com/Manuals/
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