We had a talk about this subject awhile ago (which, frankly, I'm too lazy to look for and link you to), and the consensus seemed to be that marking everything the first time through and, once you got all the way through, doing only marked questions and unmarking them as you go is the easiest way to go about it. Obviously, that has some drawbacks if you like to mark questions and go back to them, but that's nothing a pencil and paper can't fix. This idea got sprung on me a bit late, so I'm marking everything on my second pass in preparation for a third time through. Yes, really.