Did you look at the CSS documentation? You can also use your web-browser's built-in Developer Tools to view the CSS (and HTML) the story format generates for the current passage being show.
You can use custom CSS in your story's Story Stylesheet area to override any of the story format's default CSS, just use the same CSS Selectors as the default does.
The only time you should really need to mess with the source is if you want to insert custom <div> or <script> elements, or find something that has been hardcoded in jquery. Eg I am not sure if this was changed in SugarCube 2, but in SugarCube 1, altering the CSS for #ui-overlay does nothing because it always gets overriden by a jquery function.
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You can use custom CSS in your story's Story Stylesheet area to override any of the story format's default CSS, just use the same CSS Selectors as the default does.