I never made separate notes. I didn't have the time, either. It's a personal choice whether you want to /have enough time to make notes or not.
Difficulty/Importance of any fact is very subjective and the same goes with the highlighted portions. Identify the areas you tend to forget and highlight them accordingly. This will only come with repeated revisions.
Personally, I don't believe in the usefulness of READYMADE NOTES. I don't think they will be of much use in upsc untill you personalise them according to your capability and demand.
Your aim for note making should be reducing your efforts, stand out from others in content and presentation and not reinventing the wheel.
~ UPSC CSE Topper.