Very rarely do you need to have all the files in the same place, and even when it is configured as such you can still open up the javascript / css and change where things are pointing to.
But, if you absolutely need all hte things to be in the same location, if you add .js, .css, and whatever other file extensions the plugin uses into your allowed Media Content (through Kentico settings), then you can create the folder structure and upload all the files into your media library.
Downside of course is you can't modify the css / javascript through the portal if you are just uploading the files, it is best to put them in their correct spots and just modify the references (which are usually just in the css, search the css for 'url' to find where it's referencing files)