I think that in part garymardell means there’s a gazillion ways of creating a website. There’s not just one way to solve most things, there’s a hell of a lot and CodeIgniter either helps you or doesn’t stand in your way.
The user guide tells you how CI works and how to use CI’s resources, it will help you build your website but it won’t teach you how to.
There’s some CI books and some more basic PHP books or tutorials online and on these forums. Search and read those.
To start out building your app I’d suggest first deciding what you need from your website and then searching the forums and Google for different ways on implementing your ideas.