[GraemeJ]

I have never bought in to the idea of one huge file and bookmarks. My vote is to keep each chart as a separate PDF file. It might require a little more work, but you can scale each one to fit your screen size and any other modifications you might like.

That way, it's easy to annotate, make a second copy (for whatever reason) and share with someone else.

Plus, in the worst-case scenario, you won't lose everything at once.