Definitely separate notes for class vs studying. Colors can be good. Probably too hard to use different colors when taking notes in class. Once you get to the part of the class with many chemical reactions, make a list of all the reactions with reactants and products, making note of regiochemistry and stereochemistry.
Draw resonance structures every day until it becomes second nature. Also draw mechanisms every day for reactions you are supposed to know. And of course, it goes without saying you must do all the assigned practice problems, mostly without answers in front of you, and then check your answer in the solutions manual. Solutions manual to the textbook is required, unless you have tons of online homework. If you do have online homework, you also need to put pen to paper and write out the answers manually. Punching in answers on a computer screen does not help you to remember as well as writing down the problems on paper.