No. Keeping all your code in one file is a recipe for maintainability disaster. I've found that with Javascript, proper project organization is even more important than with some other languages.

It sounds like you haven't become familiar with Node's CommonJS compatible module system. Try starting there: http://nodejs.org/docs/latest/api/modules.html

Once you understand the basics of modules and requiring, I'd take a look at the ExpressJS example apps for organization ideas: https://github.com/visionmedia/express/tree/master/examples