People do that different ways. I'd suggest NOT trying to add everything from class notes into FA that isn't already there... class is way more in depth than both FA and the boards. Definitely don't add anything from class that isn't found in a relevant board review book unless you are just certain that it is something that might be tested. Yeah, everything is fair game, but you can't deal with a copy of FA that becomes 3000 pages thick.
Use class notes and other sources to add annotations to FA primarily to clarify stuff that is already in FA but not explained well or in a way that you'll remember easily or lacking in details that you think are important. For example, while people say the pharm in FA is enough it bugs me that in many cases there are mechanisms that aren't explained or even mentioned for a couple of drugs, lots of side effects and interactions are left out, and some primary uses even are neglected. So I don't plan on learning a lot of drugs that aren't in FA, but I'd like to know a few of them better than what FA covers.
Past that, there are certainly places where FA is lacking in concepts covered and depth of coverage. Neuroanatomy, cellular and molecular biology, lots of path, etc. It's up to you whether you want to try to annotate all of the extra into FA or just keep separate review sources for those areas. I'm following some good advice and have had the back cut off of my copy of FA and punched to put in a 3-ring binder. Now I can makes notes in FA, add a sheet of my own notes and/or diagrams if I need more room, or just copy a couple of pages/charts/etc. out of another source and add to the appropriate spot.
