Read his diaries making Fitzcarraldo. Reads like Heart of Darkness on acid.
Conquest of the Useless: Reflections from the making of Fitzcarraldo
I can't recommend anything in specific response to what you have asked. But I will propose something tangential that may help you get at what (I think) you are really seeking.
I recommend watching Werner Herzog's Fitzcarraldo. If you haven't seen it, it's strange, frustrating and beautiful.
Then check out Les Blank's excellent documentary, Burden of Dreams, on the making of Fitzcarraldo. Fitzcarraldo was not an easy film to make - crew members were shot with arrows by natives. Herzog threatened the life of his star. Les Blank is Herzog's close friend and was there all along. You'll get a completely different perspective, and an intimate, honest and painful portrait of the making of the film.
To complete the circle, consider reading Herzog's book, Conquest of the Useless, which is Herzog's poetic and terrifying behind the scenes account of the making of Fitzcarraldo. Even some comments about how Les Blank made Burden of Dreams.
This sounds like a lot of work. But I learned something from these three things I feel like I could learn no other way. Three ways to see one work. Somewhere in the middle is "the truth" - the essence of documentary.
To further extend the journey, consider Incident at Loch Ness. This is a "mockumentary" detailing the account of the production of a fictional Herzog work, starring Herzog. It's funny and augments some of the above.
None of these are behind the scenes of documentaries, but they present a complete picture around one director and associated works and may help you in a unique way.