My advice: Ask you regulator what format they would like have the information presented. Not only do you begin a good rapport that will carry through the exam, but you may even get them out of the bank a little faster if the information is organized consistent with how they do their on-site work. I've had regulators prefer binders and then some that preferred file folders. My preference and current system: a series of binders for each component of the exam: Service, Lending, Investments. There are cover forms describing each transaction or activity encased in a plastic sleeve within the appropriate binder, and then supporting documentation contained within the sleeve. Yes, I am duplicating some of the information that can be used in another category, but if you keep up with this throughout the year, it's not a huge deal. For example, a contribution and service activity to the Habitat for Humanity may have the same supporting documentation regarding the mission of the organization, etc. I would copy the information for inclusion in both the service binder(s) and the investment/donation binder(s). Additionally, a comprehensive performance context piece is written and presented to the EIC at the beginning of the exam as a self-contained document. Then, as a "reminder", if you will, applicable sections of the performance context relating specifically to our service, lending or investment performance are included at the beginning of each binder.
Good luck and good results!