Generally the Css is in its own document which you link to in the head of the html document. Codepen reflects this, keeping the css and html in their own separate sections, keeping everything organized, but without the need to link to the stylesheet in the html.
Css can be done internally, externally or in-line, but external is the preferred/ generally accepted method.
I don’t really know much about cloud9 yet.
hope that was of some help,