I would advise to maintain a balance when you enter Year 12. This means not just caring about academics, because while it is important, maintaining a healthy well-being is the basis to striving in academics. Do not be too hard on yourself, since there may be times during Year 12 where you disappoint yourself a little. There will always be time to improve and remember that all the way until your HSC exams. I saw Year 12 as a cumulative process and it is important to take the year step by step, that is, always make sure that you are on the track and you do not derail too backward or forward.
I know the trials or the HSC exams may seem rather intimidating as you get closer to them, but the great thing is that as you get closer to them, you actually become more prepared for them. I suppose what I am attempting to say is do not stress too much. Keep yourself on task and you should be fine. If there is anything I have learnt from looking back on high school in retrospect, it is that I was
far too worried about everything at the time and I wish I had just relaxed. Having said that, I hope your experience is more enjoyable and enriching than it is negative.
As for your question, do whatever makes you comfortable. You will probably have to organise your notes in Year 12, especially if you are doing subjects like ancient and modern history, so it is not a bad idea. Just make sure whatever method you create to operate in Year 12 is one that you stick with and are consistent to.