CSS stands for Cascading Style Sheets. In the MC software there are two main CSS files - style.css and custom.css. When you udpate font settings in the admin panel, you are updating the style.css file. Any overriding or extra settings can be added to custom.css. Any custom rules can be added to the custom.css file.

Here is a good short article on organizing CSS rules and selectors across many files.

Architecting CSS
http://www.digital-web.com/articles/architecting_css/

Found via Gadgetopia