Rather than adding CSS code to your theme you can add custom CSS for your module code itself by using: drupal_add_css.

Here’s an example of hook_init in admin_menu module:

$path = drupal_get_path('module', 'admin_menu');
drupal_add_css($path .'/admin_menu.css', 'module', 'all', FALSE);


Add a reference to the CSS path in your theme’s .info file if you want just custom CSS at the theme level