Want to learn how to server structure a 'build your website' application with Node.js

Like the title says, I am trying to understand how a build your own website / host it and append your domain works using Node.js/Express.js to structure the server and possibly MongoDB for the database.

I guess I came to Treehouse because I have really come a long way from starting and while I know this is a really advanced topic, I really don't know where to look or even look up. So I want to break this down as simply as possible.

To start this off, I understand I will need to make a REST API to handle the majority of the web application, and that isn't what I am asking about. I want to learn really how the following works:

1) I have built a simple CMS for testing purposes most of which is REST based. With services like WIX / Squarespace, are they having users save templates / files to a shared storage and are associating these templates / websites with only the user and then accessing them once the associated domain is called? Sorry, I feel like I am complicating this but how would one let users customize a template and save it uniquely to them? Where are the files stored? Do you generate a unique folder structure for that user and some how save the associated files to the user? Yeah, I am lost at this point... Sorry :/

2) Once the user has their template / little shop set up, how would you let the user set a domain to their template they worked on? Here, I guess I would love a reference on how domains work and how you could let your users point their custom domain to your application and further more, their specific template of that application.

This is a lot and I am not expecting a straight answer really (although it would be awesome if you did), but would love some references to where I could start learning this stuff or even what the proper way to ask about this would be. Thanks everyone! Hope someone can help!