The common method for doing what you're looking to do is to run them side by side, and either proxy requests from apache to node.js based on domain / url, or simply have your node.js content be pulled from the node.js port. This later method works very well for having things like socket.io powered widgets on your site and such.
If you're going to be doing all of your dynamic content generation in node however, you might as well just use node.js as your primary webserver too, it does a very good job at serving both static and dynamic http requests.
See: