There are lots of question to ask how to customize , where is html code of template ... Ya! It's T3 blocks.
We can check it in:
There are lots of blocks here but we can focus on:Code:plugins\system\jat3\jat3\base-themes\default\blocks\
This block will use for generate Joomla! <head>. So you can put your jQuery include here as safety init.
Another else blocks could / often override depend on each template.
Just let's me know if you have any else question about blocks !