node.js deployment questions
So, you probably won't be able to use Node.js on a typical 'hosted server'. These servers are typically running Apache and only support a limited set of languages. There are several providers that offer Node.JS hosting, including the creators: Joyent.
Otherwise, you'll need control of the actual server so that you can run the node myapp.js command. For a list of possible providers, see here.
Once you get the app running node myapp.js, it should start handling incoming web requests, just like any other web server. Now, if someone is using nginx, they're probably using it as a load-balancer or to serve static content.
If you don't understand how or why it's configured this way, you definitely need to talk to the project owners. The rest of the details depend completely on where / how you're hosting and the answers to the nginx questions.