How do I effectively annotate my texts for later study?

This seems like quite a simple question with an obvious solution, yet when I sat my GCSE's I remember struggling to determine what was important in a text to annotate or underline for future reference. Consequently, I underlined almost everything and my text became so convoluted I no longer wished to read it!
When reading your text for the first time, you can start off with the first three categories which are setting, character and theme, underlining quotes you think convey something important to either one of these categories. Then this can be adapted to underlining quotes for a specific theme, character or setting. For some quotes it is obvious why you underlined it at the time but for others it is important to leave an annotation stating why that particular quote caught your attention or how it is relevant. To this day I find annotating my texts very helpful, especially how I do it, because when you revisit a text later on in your course or close to exam time you can compare the perspective you had when first reading the text to having read it a few times. What has changed this perspective? Is it the context or perhaps some bias developed from further reading?