Color Scheme Every Theme Pluggin

This pluggin concept is awesome but I am confused with step 2 of the installtion process, customizing the FUNCTION.PHP file. I have installed the plugin, activated it, clicked the generate button and the color schemes changed in the customize tab. This is where I am stuck. There are several function.php files. I am using a Local Business Theme, therefore, I would imagine you update the function.php file located under the Local Business Theme. Second questions, once in the function.php file, where in the code do you insert the two snippet code sections found in the installation process. Your help would be greatly appreciated.