All your code in Coffeescript will be inside a self-invoking anonymous function.
To call it outside a file, just write:
window.square = (x) -> x * x
alert(square(5))
in an other function
The best you can do to not overuse window is a App object that will contain all your variables.
window.App={}
window.App.square= (x) -> x * x
and then alert(App.square(5))