The color you select is being applied to elements in the "header.php" template file. Just locate the CSS in the header and replace the PHP function with actual CSS to customize it the way you want.

Hi Chris,

How to exclude certain element being formatted by color theme chooser?

e.g. i choose blue color(from option tree) as the theme colors, but i want red color for the navigation link and sidebar accent instead of being formatted as blue, so i can define the navigation link and sidebar accent colors manually in the CSS file, could you please pointing me out how to do this?

Thanks in advance.