Alright this seems simple if i understand what you mean....
CSS=Design of the Webpage
<script>JS/JQ codes go in here</script>
as you can see we add the "<Style></Style>" tags before and after the CSS code
<style>CSS codes go here</script>
You can also Link them to your html page (in order to keep everything organized: 1page for all html, 1page for all JS, 1 page for all JQ, 1 page for all CSS...)
That way your computer automatically knows were to look and all the style and actions are applied to your page!