The next, crucial stage, between reading and writing, is planning. Essays that have been planned are better than essays that have not been planned. You should plan essays both for supervisions and in exams. It only takes a few minutes. The first and last sections are always the same: 'Introduction' and 'Conclusion'. The intervening sections (normally a smallish number of them, in the region of 3-5) should be arranged in a logical order so that the essay reads smoothly and clearly. It should always be clear when you are moving from one section to the next, and how and why you are doing so.
At various points both before and after the planning process you will need to read through your notes. Once you have made your essay plan you might find it useful to go back through your notes and mark the particularly important parts in the margin with the number of the section in your essay to which they will be relevant. Or you could use colour-coding, making a different coloured mark in the margin of your notes to indicate the different theme or section of your essay to which they relate.