Maintaining a structure for notes can be hard. I'm using a simple "Inbox + Archives" structure.
Having no structure whatsoever, letting the notes slosh around randomly, relying on the magical savior to rescue me.
已弃疗
Using Keyboard Maestro for shortcut, although you can use OS X's built in function to set keyboard shortcut(globally).
Evernote lack of support for code highlight has been a real problem. The idea is to use it's support for RFT to support code highlight.
In order to make it work, you'll need highlight installed.
brew install highlight
Then move Highlight.applescript into your ~/Library/Services folder. Shortcuts can be set in System Preferences - Keynote - Shortcuts.