Footnote.js is actually written in CoffeeScript, so you need to install coffeescript and then compile it with coffee -c. Alternately, pester me enough and I'll just put the compiled version under version control, even though that doesn't really make semantic sense
Just make an element with the class "fn-document" and then have elements with the class "footnote" contain footnotes. If you want to denote where your footnotes will appear, denote them by making an element of the class "fn-holder" somewhere in your fn-document element. Otherwise, it'll appear at the bottom of your element.
That's pretty much it. Good luck.