> Does anyone who knows enough JavaScript point me in the right direction about it. I find all this very confusing.

There isn't a straight forward solution, but the closest for me is the combination of using a transpiler (Babel), and a bundler (Webpack).

A common criticism on node/javascript projects is the boiler plate setup required. As far as I know, there isn't an IDE that takes care of doing this part for you, where your experience developing outside of the web might (I like to think it akin to starting a project from scratch with C++, gcc, and make).

Some larger projects, do have scripts that do a lot of boiler plate for you, such as Create-React-App. https://github.com/facebook/create-react-app but that is for a specific use case.