How do I organize? Badly, and in my own idiosyncratic manner, I fear. Which is why we didn't go this route, quite honestly. I was just not good at doing it aggressively enough. People I've known IRL who have done it, though, keep capstone "projects" or documentation of them (multimedia, digital photos, etc) on a yearly basis, updating the master files every so often with new additional material. There is also often a "notebook" that documents day-to-day activities in a more cursory manner-- but basically shows what the student spent time doing.
Test scores, etc. are also a part of that notebook (digital photos may be formatted and included along with url info to a youtube video or other online source of the full presentation, as appropriate.