For example: if you are using beez_20 template, then your javascript file will be first loaded from here: www.yoursite.com/templates/beez_20/js/com_koparent/krcommon.js

First you can just copy those files to your template folder.

Getting a head-start with editing the javascript files

If you are new to Joomla! development, then it is probably easiest to start with the krcommon.js file, and try modifying it to get what you want. To do this, you should make a copy of the existing javascript file in the js directory of your template, and then modify the copy.

The directory structure you need is:

TEMPLATE_NAME/js/com_koparent/FILE_NAME.php

For example, if you want to change the 'krcommon.js', then you should copy the file at

PATH_TO_JOOMLA/media/com_koparent/js/krcommon.js
to
TEMPLATE_NAME/js/com_koparent/krcommon.js

(note the slight difference in directory structure)

There you can see how simple modifications can make big impact on the site and how it is easily changed. Note: When you are making modifications in your template folder you do not have to worry about upgrading Koparent extension, it will never override your modifications in template folder.

Further tips

For the FireFox web browser, an extension called Firebug is available, which is useful for browsing a page's HTML source and matching it up with the PHP code used in template overrides. Now firebug is also available for IE called Firebug Lite.