Theme Updates

When you update the theme, the header.php file is often updated, is that correct? I have code in the header.php file to track customers on site. In the Highend Options, there is a space for the Google Analytics script. But I also track customers for marketing automation purposes. If I add it to header.php, when it gets updated I have to re-enter the code. Can I add the script in the same place Google Analytics is located in the Options settings?