After I finish the first draft, I go back (on the computer) and plug in any notes. I no longer write with an outline, so as I'm writing the draft, I keep a list of things that have changed since the early chapters, places I need to add foreshadowing (things like that). Once those notes are finished, I'll print it out.
I heartily recommend that folks look into a laser printer. The cost of the printer v. buying new ink refills for inkjet printers is so worth it. My printer retails for about $120, and the toner it came with is good for 5000 pages. Toner refills cost about $85. It more than pays for itself.
I also save money/ink/paper by reducing the font to Size 9 and printing 1.5 spaced, rather than double. My eyes can take it, and I still have room for editing notes (I have tiny handwriting). It makes a 380 page document a more accessible 210 pages.