Once logged into your GCSE account visit this link http://support.google.com/customsearch/bin/answer.py?hl=en&answ...
In short it states: "The free version of CSE includes advertisements, mandatory Google branding, and fewer customization options. In order to disable ads on your free CSE, you site must belong to an organization recognized as exempt from taxation under section 501(c)(3) of the U.S. Internal Revenue Code. Outside of the U.S., this is available to charitable organizations as defined under country-specific regulations or requirements, but would need to upgrade to Google site search for the other features of business edition."
For assistance with code placement in your OU templates, please submit a ticket to our Helpdesk and a technician will be happy to assist you. firstname.lastname@example.org
I hope this helps