As a newbie webdev, what would you suggest? Making an API-based web application? (the backend would serve and receive JSON and the front-end would simply play around with it) Or am I completely misunderstanding this.
That's a reasonable way to build an application, and one that I personally prefer, but there isn't a silver bullet. But if you're building a Node app your server js and your client js don't need to commingle. Make a src/js/client directory, and stick your package.json in there (if you want to use this tool).