The notebooks represent my highest level of organization; everything lives in a specific notebook (e.g. Clients), then each note is part of a stack that represents the work being done with each client, then I use tags to discriminate between various projects (e.g. a website and a brochure). This enables me to search both at a high level by just searching notebooks and at a more granular level by searching tags. So I can quickly go from looking at all of my clients to looking at all of my, say, web projects.
Make sense? Happy to answer any other questions and have a Sweet Sixteen!