[iraphael]

i would focus on just taking notes on related topics, without much structure for a bit. try to link them together if they are on related ideas a bit. once you have a network of notes that feels a little less manageable (~100), i create a "map of content" where i link to all notes related to that concept, and in it i essentially tell a higher level story about how those notes relate to each other.

[lolcat_cowsay]

This is if he wants to take notes in the first place.