Colors to my header and footer not applying by using color scheme options in my theme
I am able to apply css for my header and other things, I found an alternative way to include the css.Even though I can't find a way through drupal_add_css(), the following helped me in adding css.

This is the way I included dynamically generated css file which is located at sites/default/files/color/theme-768/color.css

In the theme folder in the html.tpl.php after &lt;?php print $styles;?&gt; include this

&lt;?php    
       print '&lt;style&gt;';
       print '@import url("' . $filepath . '")';
       print '&lt;/style&gt;';
?&gt;


This includes the css file and provided colors for header, footer etc.