What and how are you annotating? Are you writing down every single detail about, let's say fatty acid metabolism?
To be honest, I haven't exactly started annotating stuff into FA yet. I'm just going through Kaplan Biochem and Rx right now. I wanted an idea of what and how people are annotating since I'm not exactly the "writing stuff down on paper" type of guy.
As you go through World, I'd add in any discrete facts / concepts that aren't in FA... in micro, for example, if they mention some symptom or test associated with a bacteria that isn't mentioned in FA, I would add that. Another good example would be pathophys... if they mention some concept that isn't in World or BRS, I would add that. Lengthier stuff, like the process of fatty acid metabolism, would be harder to add in a clear format and probably too time consuming even if you wanted to. I'd keep my notes short and to the point, saves time and easier to go back and understand what you wrote.