You can enter small amounts of custom CSS by going to
Graphene Options >> Display >> Custom CSS
(it’s at the bottom). Just enter your custom CSS and click the “Save Options” button.
For large amounts of custom CSS, you should use a child theme. You can read about how to create one in the theme’s wiki here:
http://wiki.khairul-syahir.com/graphene-theme/wiki/Customisation_using_a_child_theme