Hi!
That's a great question! When I did the comparative study, I had my notes revolving around the comparison between the two texts because it made more sense to me since that's the premise of the module. I think to make the notes separately, while it can enable you to go into more depth, will only make extra work for you later on. You'll have to draw connections between the two texts on top of having to cut it down to what you think the best examples are to bring into the exam. You will be restricted to key ideas and quotes if you take the former approach but you'll know for sure that each text is being considered with the other in mind and that you'll be able to facilitate effective comparison at the end of the day. Ultimately, your aim is to explore their "textual conversation" so I would definitely argue the former is the better way to go!
If you would like to see a good sample of it, here's my notes - structured in the way explained above.
I'd also recommend using your study notes in combination with practice questions! Once you have your content consolidated in one place, I would highly advise applying it to questions. Hope that helps and let me know if you have any further questions