Setting up a MEAN stack on server

I'm working in a company that has been developing websites with PHP and thus we have been using a Rackspace cloud server to host our files. I want to bring us forward in time and try to develop our new site on our server using the MEAN stack. I've had quite some experience building sites using MEAN, but my previous workplaces used ready-to-go services such as nodejitsu or openshift.

I've been googling for examples, but found none so far. I could really use some knowledge and references from those who's had and experience in setting up node and mongo on a private server. To put it into perspective, this is a server that runs Apache, and I control this server using WHM, cPanel and SSH. I need to run the website as a subdirectory.

The server's OS is Linux, and I have access to the root user.

My biggest questions are:

1. How will my app.js listen to incoming requests, if I want to run it as a subdirectory.
2. Locally we can run npm start to start the server. On nodejistu this happens magically as we push the code. But how do I do this on a server like mine?

Thanks a lot in advance.