I just received the copyedit for GOD and I have to say I don't know how I ever lived without Post-its.
Here's what works amazingly well for me:
I read through the entire manuscript, and if I can't make a decision in 60 seconds on a copyeditor's question or something I think needs to be tweaked I slap down a post-it and move on. Once the manuscript is done it might contain 150 Post-its. The second time through I just read the flagged stuff. This allows me to completely focus on the problem. I can usually make a decision in less than a minute, and am able to remove the sticker. If not, I leave it and by the time I'm finished with that round I usually have around 20 Post-its left. Repeat the previous trick and that usually takes care of them all. I've used this method for the last three books and I'm still amazed by how well it works.
I've also had this copyeditor before and she's excellent. With some copyeditors you might spend a lot of time trying to decide if something is worth fighting for, but there's none of that going on here, which makes the process pretty painless.
oh, I've added a link to the previous post in case anybody wants to watch the video about the little pop-up trailers.