This is a great question. It would be great to hear what the intentions were from the MOD team.
I don't know if I'm actually doing it right but this is what I'm currently doing.
Input - Using the the controls on the DUO, I set a level so that it went orange/yellow when I play the loudest.
Output - I set it to 0db (wide open). On my pedalboard I use the Gain plugin at the end of my chain and assign it to a knob. Two reasons I do this - 1. I'm finding that each plugin's output works differently. Depending on how you are using the effect you can lose level and the level knob doesn't increase enough or the level is so hot... So I use the Gain plugin to cut/boost in many places. 2. It's faster to access the output level if I have it assigned to a knob.
I'm interested in how others are dealing with their input and output levels.