Personally I only anotate from USMLE World into First Aid. If there is a question or explanation that I didnt know and that isn't in First Aid, then I put it in there. For me, I actually type it into a word document, and when the word document is full I print it out and put it into my FA book which has been unbound and 3 hole punched. Also, if a professor tells us that such and such fact is constantly put on the boards, and its not in First Aid, then I put it in.
Otherwise it would be too much to put all the details from our class notes into FA.