Yes, keeping a journal is very much learning what you need as you go, because everyone will be different. As your last sentence almost says, it's the sitting down and thinking about the book later that's the important part, actually writing down your thoughts in a journal is almost an optional extra - but I would not have the discipline without the journal to enforce it.
One thing I found works well for me is placing a hard limit on how much I write. Since I am such a naturally verbose person, this really makes me think hard about what was important. (It's also good practise for my own writing.) It has the added advantage of making it more likely I will re-read the entries
.