It's really simple. You've got an html page. But, you also can use external files... just like you'd use an image.
The .html page doesn't include the image, it says <img src="image.jpg"> where "src" means "source"... source file.
<script language="javascript" src="js.js">
Honestly, I can't remember if that's the right syntax, but it'll show you how on the scripts pages.
Just follow the example.
css is just a formatting file... that you tell your html page to use.
basically... js and css can be included in the text of the html file, or 'linked' (referenced) to in it, then saved seperately. (Actually, there are some methods of having different parts of webpages in different files, but that's more complex, depending on the method.)
Make sense?
I'm sure it'll tell you how to reference them in the specific script page.
Also, you probably need to put the files (.js and .css) into the same folder ('directory') in your ftp (or free site's default upload system, depending).
Got it? :)