I figured out my humidity issues!
You have to configure which life support units you want in individual pods.
When you right click on a pod it will say 'Configure Pod' which lets you choose 2 of 4 options, "Scrubber, Pressure Control, Humidity Control and Water Recycler"
When you unlock the external ECLSS part you can also choose these options so you can have all four. Still testing so I don't know if you can have a ship with two and two and if it will work.