Hello,
we have recently prepared a sample project where Atlas works with Kentico CMS. If you want to use AJAX with Kentico CMS, you need to have <add key="CMSFixXHTML" value="false" /> parameter in your web.config and you can use only static <head> section in you HTML code.
If you want to test it, please download the following files:
Code: http://www.kentico.com/downloads/atlas/KenticoCMS_1_9_TestAtlas.zip
Regards,