The templates that come with the installation of SOS Webpages are Free Software and can modified however you wish.
I'm no lawyer, but the terms of the GPL do not allow you to make a derived work that is not also free software. But any template you make yourself would not have to be released under GPL or other open source license. When making your own template some parts of the code would be identical, because they are basic php. For example:
<?
//This section builds the main menu
//Each menu item will be defined by the text in the variable below
$menu_item_divider = "</li><li>";
$pathFix = dirname(__FILE__);
include("includes/menu.php");
?>
Using this piece of code out of 'templates/99blue/template.php' is probably not a violation of the license. I doubt using anything inside that particular template.php is completely original. Going into the stylesheet and just changing the colors would not produce something that you could copyright.