It's a very different cognitive task than writing it. I like to keep them separate. I put in the notes but I don't worry too much about the exact page numbers and other details when I'm writing. It's a fiddly job and it's very inhibiting of thought for me. I just have to trust that I'm going to do it later.
But now that I'm doing it with Hyperobjects, I'm finding it very pleasant. I do have to check through some things to make sure I put them in. Then it's almost good to send I think. I'll read through it a few times for style.