There are a number of common ways of doing it - my favourite being a project called ng-boilerplate [1], which encourages you to create directories based on features, and then place all the files related to a specific feature (tests, javascript/coffeescript, html, css) in the same directory. It uses grunt to compile the various files into a single file as you are coding.

Another good resource is a well made example app called angular-app [2], which includes security, a small backend, some crud pages, etc.

1. https://github.com/joshdmiller/ng-boilerplate

2. https://github.com/angular-app/angular-app