We both use evernote for business and personal notes so are very used to the system and its benefits.
Our preferred approach is to organise notes through using the awesome tagging system.
You can have multiple levels of hierarchy and can search very easily.
We both started out on the notebook based system but searching is time consuming and you can only have one level of hierarchy.
Anyhow, we use it for all our planning notes for our round the world exploration.
It is organized something like this with the highest level being: rtw ( always use lower case for simplicity of searching)