Evernote user bluecockatoo did a lot of thinking about how Evernote could easily and reliably fit into his day-to-day workflow, much like our own editor. His publicly visible "EverMetaNotes" are a wealth of answers what-about-that Evernote questions.
Bluecockatoo struggled with many of the same issues as Whitson — keeping a handle on his notebooks, figuring out how Evernote fit into his to-do structure and more. When he came up with a good solution, he posted it to Evernote. For example, how to separate his personal and work Evernote use:
But in that case I log into the web interface for my personal account and use the Evernote bookmarklet (not the FireFox plugin) to clip to that account. The FireFox web clipper will post things to the desktop client of my work account. So it's basically two clicks if I want to save something to both places from the browser.
There's a lot of Getting Things Done, a good bit of tool and setting tweaking, and some good general advice on what Evernote is really for, at least for one avid user.
Evernote shared notebook: EverMetaNotes [Evernote]