Use these docs as a reference for all the available components and piece together the pages of your app. Customize the style too - make the prototype all your own.
Read about push.js then start connecting your pages. Push.js allows you to create a prototype that feels like a real app when you save it to your phone. (Need to have a server running).
There are a few ways to do this, but the simplest is to run a local server on your computer, point Safari on your iPhone to your computer, then click the button and "Add to Home Screen".