I print out the full manuscript at 1.2 line-spacing with a wide right margin of 3+ inches. In other words so the text block appears more closely the way it appears in a printed book. I can’t remember how long I’ve been doing this but I know I started doing it because of a manuscript page of The Great Gatsby I’d seen in a biography of F. Scott Fitzgerald (and misremembered):

The wide margin works because I tend to write longer notes and the standard double-spaced manuscript format leaves little room. Before I would change the document back to standard format after printing but this week I wondered, Why not just leave it? So I left it.
I sit on my couch with the printed pages and a pencil, and bracket out sentences and paragraphs along the way that need to be removed, rethought, or rewritten. When I’m couch-reading I’m looking for plot, flow, thematic resonance. I’ll correct typos and missing words but try not to rewrite sentences as I find it too easy to get caught up in the details; sometimes a comma will tend to feel either missing or superfluous depending on the mood I’m in. Instead I scribble notes about what’s missing from a chapter, or about the role of a paragraph: to introduce X, to echo Y, to make joke about Z. Basically, an ex post facto outline (which is the only kind of outline I really find useful). This helps me see past the sentences and paragraphs I’ve grown attached to – like, I’m literally just reading down the margin – to the reasons they exist.