This describes how I setup Atom for an ideal Clojure development workflow. This fixes indentation on newlines, handles parentheses, etc. The keybinding settings for enter (in keymap.cson) are important to get proper newlines with indentation at the right level. There are other helpers in init.coffee and keymap.cson that are useful for cutting, copying, pasting, deleting, and indenting Lisp expressions.
The Atom documentation is excellent. It's highly worth reading the flight manual.