Hi there,
If you wanna add script/code, you could try with overridding default.php file of JAT3 plugin for your default template and insert your script/code inside as follow:
Copy the file plugins>system>jat3>jat3>base-themes>default>page>default.php into templates>ja_your-template-name>page>default.php and insert your analytics code just before the </head> tag as per below.
<head>
************YOUR SCRIPT HERE *************
<?php //gen head base on theme info
$this->showBlock ('head');
?>
<?php
$blocks = T3Common::node_children($this->getBlocksXML ('head'), 'block');
foreach ($blocks as $block) :
$this->showBlock ($block);
endforeach;
?>
<?php echo $this->showBlock ('css') ?>
</head>
