I have restructured my Evernote several times over the years, addressing shortcomings that I've identified. I'm always trying to find a way to simplify note taking and think I've got a good structure in place.
My current layout has a notebook titled .inbox where the bulk of my notes go in to initially. Any note I email, scan or snip goes in to my .inbox notebook. I then process these notes and move them into their appropriate notebooks, tagged accordingly.
I keep a register notebook where all of my bill statements and receipts go. I tag each item as either Bill or Receipt so I can differentiate between them. Most of these notes are scanned in, but some of them are emails. Such as an online bill pay confirmation.
I keep a Journal 2014 notebook and a Journal Archive. After each year passes, I move the notes from the notebook for that current year into the archive. These notes consist of personal notes I keep that pertain to my life.
The biggest organizational issue I have is with clippings. They range from development white papers & code snippets to news articles and paperless blog posts. Trying to figure out how I want to categorize and preserve these clippings has been a bit of a challenge. Tagging can help with a lot of it, but I'm not sure if I want to store them in a single notebook or break them down. They're broken down right now, but I'm not happy with it. I've almost gone to granular with it and need to lump some of my notebooks together.
At some point in the future I will need to do a more in depth post on how I capture my content, what apps I use and how my tagging system is set up.