To configure CSS for the Admin Area, you have options. You can use the css_injector module, or simply modify an existing css file.

Regardless of the location you are going to store the css, to modify the administration are, use the class .logged-in to target the backend. Example:

.logged-in #container { background: orange ; }

The previous css definition would cause the background of the administration overlay area to be displayed as orange. Using .logged-in, you can target any area of the backend.