Mary, I'm not a professional editor, but I did get paid to crit/edit a friend's novel. (She insisted on paying, even though I would've done it for free for a friend.) My method was basically to make any small-ish comments (or fixing typos, which was the main reason she wanted my help) in the document itself, in Track Changes. Then I had a separate .txt file where I would make any larger notes as I was reading. So things like, "Hey, in this chapter X happened. Does this mean Y will happen later? Because I'd be disappointed if Y didn't happen (or if you want Y to be a big reveal, then maybe you need to cut a few details from X), etc." I find first impressions to be really useful, which is why I made all those comments after each chapter. Then I made overall comments at the end of the novel read-through - big comments, the sort of thing you tend to expect from a critique.
Does that help? It took me several weeks to get through it, because I would only do a chapter or 2 per day, and I had some other things going on, and yeah - I found I wasn't forgetting anything important. If memory serves, I would sometimes read back through some earlier post-chapter .txt-file comments to refresh my memory, but didn't need to do that too often.