Editing

I’ve tried–repeatedly–to figure out some method for editing my manuscripts. Not the line edits–word choice, sentence rhythm, the notes let’s say–years of writing poetry have helped me there. 

No, the story structure and chapter/scene level edits seem to well pick your cliche: slide through my fingers, something something wisp, something something phantom. 
I just can’t seem to get them to make any  sense in my head. 
There seem to be two major schools if thought: 
1. Print out your MS and mark it up with stickies and a pencil;
2. Draw pictures. 
Now. I’m bad with THINGS. I’ve spent the past five years of my life trying to get rid of objects. Data is fine! Virtual stuff–I can organize that. But give me a physical object and I’m frozen. 
And I’m a word person. That whole info graphic thing? It’s easier for me to read a spreadsheet. 
So, I’m a bit loath to print out a ton of paper. I’ve done it, but it’s just confusing me more. Also, reading a bunch of 8 1/2 x11s or A4s (work has accustomed me to translating to the British from the American) well, that’s unwieldy at best. 
But as always, Scrivener to the rescue! 
“What if,” I thought, “What if I made my first draft into a mobi. And sent it to my Kindle? And… Used my Kindle’s notes and highlights…?” 
Oh. Yes. That.