The bulk of the CSS in Moodle 2.9 can be found in
which is derived from the LESS folders found in the 'moodle' directory here...
You can also find CSS in a file called style.css within moodle/mod/ ( under each separate mod)
Same goes for moodle/block (under each separate block)
as well as other directories within Moodle such as moodle/grade/report/grader.
In other words CSS is peppered all over the place and so easy to miss or duplicate which is one of the biggest problems we face in Moodle.
To make Moodle read your CSS is to add it to the theme you are using. That is to say add it to
moodle / theme / mytheme / style / mytheme_styles.css
Then you need to add the CSS file name to your theme's config.php
$THEME->sheets = array('core_styles', 'someother_styles', ' mytheme_styles ' );
making sure it is the last in that list.
If you get stuck please ask again for help.