Thank you all for the advice. If anyone cares to know - this is the way I solved the challange:
Because I needed to have a central place to decide what css goes on top and an additional requirement for being able to share sum function everywhere - I have extended the CWebApplication. This required me to change the index.php and instruct to run the web app using my extended CWebApplication class.
In order to problematically add/skip the inclusion of css/js files on top using the extended CWebApplication - I have extended the CController class and used this extension onward.