Ok, so heres' the thing.
NPM: Node JS package manager, helps you to manage all the libraries your software relays on. You would define your needs in a file called package.json and run npm install in the command line... BANG your packages are downloaded and are ready to use. Could be used both for front-end and back-end.
resource: https://www.quora.com/What-are-the-differences-between-NPM-Bower-Grunt-Gulp-Webpack-Browserify-Slush-Yeoman-and-Express
Now, here's where NPM stops and his dear friend Gulp takes over. I can't type all of it, but to have your css and js files in a folder (and do whatever you want with them) you'll have to use an automation tool (I personally use Gulp but there's a bunch of them out there).
It's easy to set up and the documentation is here:
https://gulpjs.com/
Gulp will basically be responsible of how and where your css files get compiled. It will base its requests for packages in the node_modules folder. So you're good to go. Configure gulp and you should be on your way.
There's also webpack. Never used it, but it seems to be the future of automation:
https://webpack.js.org/
I'd suggest using webpack.