Where do I insert code into the header? I recently updated my Drupal 'Newsflash' theme but one of my javascripts stopped working. I contacted the writer of the js script and he suggested that my head section has lost the markup for importing the overlibmws.js file, and that I should put it back.

&lt;script type="text/javascript" src="/files/overlib.js"&gt;&lt;/script&gt;


Where do I go in Drupal 7 (Im guessing it is a tpl file) to insert this code into the header?
What you are looking for is html.tpl.php which by default is part of the system module. Copy the file to the location of your theme and add your code. The copy should take precedence over the default .tpl file. 

Warning: Do not hack the core! I.e. if you add this change directly to the system module file it will be overwritten with the next update. In fact even adding the file to the third party theme is not a very clean solution (for the same reasons).

Consider using drupal_add_js() instead (requires custom code).