The book (and McPhee’s writing in general) uses these really powerful juxtapositions of place and character to convey complex themes.
In this recent interview, McPhee discusses how he structured this work using the same method he learned in high school. He essentially sits down with his notes and tries to come up with a lead. Then:
Once I’ve written the lead, I read the notes and then I read them again. I read them until they’re coming out my ears. Ideas occur, but what I’m doing, basically, is looking for logical ways in which to subdivide the material. I’m looking for things that fit together, things that relate. For each of these components, I create a code—it’s like an airport code. If a topic is upstate New York, I’ll write UNY or something in the margin. When I get done, the mass of notes has some tiny code beside each note. And I write each code on an index card.
The interviewer then asks him how his work on Encounters with the Archdruid began, and how many index cards there were:
..I knew where I was going to start, but I didn’t know the body of the thing. I went into a seminar room here at the university, and I laid the thirty-six cards out on the table. I just looked and looked at them. After a while I was looking at two cards: Upset Rapid, which is a big-time rapid in the Colorado River, and Alpinist. In Upset Rapid, Brower doesn’t ride the rapid. Why doesn’t he ride the rapid?
His answer to Floyd Dominy [Bureau of Reclamation commissioner infamous for his initiation of dam-building projects] is, “Because I’m chicken.” That’s a pretty strong scene. What next? Well, there are more than seventy peaks in the Sierra Nevada that were first ascended by David Brower, hanging by his fingernails on some cliff. “Because I’m chicken”?
This juxtaposition is just loaded with irony, and by putting the Alpinist right after Upset Rapid, in the white space between those two sections there’s a hell of a lot of stuff that I don’t have to say. It’s told by the structure. It’s all crackling along between those two things. So I put those two cards side by side. Now there are thirty-four other parts there on the table. 
How do you work out structure in your narrative nonfiction writing?
Have you ever used index cards?
Do you still use writing lessons you learned in high school or have you evolved your system?
Do you have an actual system / structure you use or does it vary from story to story?