Template folders are located in application/views folder with 2014 folder being script default template.
In each template folder we've added "custom" folder where you can place modified templates and CSS. In previous versions, if you've modified for example header.php template file and new version brings modified header.php, the upgrade to new version would completely overwrite your changes so if you didn't have them backed up, it would be a disaster. Now, if you want to modify header.php, simply copy it from application/views/2014/header.php to application/views/2014/custom/header.php and make your modification in this new file (in "custom" folder).
The script will use this new file instead of original one. Then if there is a modified header.php in the new version, your script would still use the one in "custom" folder. Maybe you'd need to adjust your custom/header.php to work correctly with the new version of the script, but at least you will not lose it and you'll have both new version and your custom version so you can compare them and find out what's added/removed.
Unlike templates, there is no way to replace CSS files elegantly, but if you make "style.css" in your "custom" folder (custom/style.css) it will be loaded after all other CSS styles, so you can define your custom CSS styles there. Like custom templates, this file will never be overwritten by the new version upgrade.