I want to use the following template for my coffeescript express app
https://github.com/twilson63/express-coffee
However I am unfamiliar with express and the app/ directory has an index.js file that seems to run the server. what would be the correct code structure to add actions/controllers/routes to this template
I think you should check out skeleton. It's a package that generates a CoffeeScript application template for you and makes use of MVC. I did find, however, that express-coffee has a pretty good cakefile (though it seems to depend on global packages too much for my liking). I combined ideas from both and wrote frappe. It's a template very similar to the output from skeleton, with a few things tweaked for my personal taste. Anyway, have a look at those - hopefully you will find what you are looking for.