For all Joomla 3+ templates built using the Zen Grid Framework v4 (any theme after October 2014) please refer to the Zen Grid Framework v4 documentation.
The Extra Scripts option in the Zen Grid Framework inserts whatever you place in the text area into the head of the template after all of the other scripts have loaded on the page. This option is useful for those users that want to add extra javascript, css or anything else to the head of the template but they dont want to dig around in the template code.
The image below highlights how easy it is to add new code to the template without getting your hands dirty.
In order to maintain any jQuery scripts running in noconflict mode please ensure that you replace any $ elements with "jQuery". Also please do not load the jQuery library or even the mootools library in this option as jQuery is loaded via the JB LIbrary plugin while mootools loads in Joomla by default.