Looking at multiplayer systems to use with node.js I don't know what communication method / library is the easiest to use.
I want to be able to have some kind of client / server authority system which is done via PHP. The user logs onto the account management system using PHP and then the User launches the client which is written in javascript that connects to the node.js server.
My question is how do I do this client / server communication and with if suggested what library. I have seen socket.io and now.js but both only have examples on how to use it without authority.
You can have a look to BrowserQuest game by Mozilla. It's open source, and it does exactly that.
Here is the official documentation on authorization
You haven't given nearly enough information on the type of game or the type of communication you need. You've mentioned Socket.IO and Now.JS, but are those a requirement? What about standard http ajax requests? Then you'll just rely on the cookie provided by the PHP session and authentication. Is there a good reason to introduce node.js to your stack in addition to PHP?