How do you revise?

With the June session of Camp NaNoWriMo under way, I've been working on revising last year's novel.  I decided that in June, my goal will be to go through the entire manuscript and mark up the changes I want to make.  Then in July, I will make the changes.  I'll also be working on some remaining research during both months, though I think that might fall more into July's to-do list.

Revising a novel is infinitely different than revising an article or a blog post.  For the shorter things, I tend to revise a bit as I go, and then give it one last read-through on the computer when I'm done.  With the novel, though, I'm starting out by doing it the way Stephen King suggests in On Writing -- reading through the manuscript, marking changes, and then making the changes once I'm done.  The only difference is that since I want to be able to work on it on the go, I am marking up the manuscript in a PDF reader on my Nook.  It's much easier than hauling around a 300-page manuscript!

I'm not sure yet how much I like the method, though, and I am still in the process of figuring out what works best for me.  Therefore I am interested in hearing from other writers: How do you go about doing revisions on a longer piece, such as a novel?