mdBootStrap and NodeJS Directory Structure Inquiry

I've read over the documentation and I cannot seem to find a clear answer as to the proper directory structure for a node application (insert downvotes here).

When I create an application directory off the root. All js, css, and img directories will be based of this application directory. My confusion comes in where when I install mdBootStrap using npm it creates the node_modules and mdbootstrap directory as expected, but then down these chains of directories it creates it's own js and css directory as well.

So back in the main application directory, in the HTML files, when I reference bootstrap and jquery files for example, am I forced to reference all the way down the node_modules directory, or has the mdBootStrap actually become my new application directory.

via Spades