For example, I created folder, opened it with VS Code. Opened a terminal, used the command npm install jquery, it creates a folder node_modules within my created folder. I then create an HTML file, put HTML template in and now I want to reference jQuery. I know how to reference the files syntactically and all that, I am just looking to understand best practices.
Do I just reference jQuery... JavaScript files within there? Or am I missing a step?
before starting on a new project you should use npm init. this will initialize the project and generate a package.json file. This package.json file is used for managing the project's dependencies(libraries), scripts, version etc.
And after this every time you install a library using npm it will get listed in this package.json file under dependencies section.
example after initializing the npm:
npm i jquery
and you can get it using
const jquery = require('jquery')
or
import jquery from 'jquery';
i.e; without using the relative path, example:
import jquery from '../../node_modules/jquery..'
It sounds like you are missing the build step.
When developing with npm, you usually use a toolchain with compilers, bundlers and minifiers, which read the libraries from the node_modules folder and put the resources in a build folder which actually gets deployed, and from where the js file will be loaded.