As mentioned elsewhere in the site, this framework runs with a set of core templates and skins.
These are the files that you will adjust on every site. Here is a reference detailing the skins' files and code.
This is the extension that provides the code needed for the framework. You should never adjust the code directly in the extension. Things you might need to adjust (like in the page object) can be overridden by TypoScript.
But if you need to satisfy your inner geek, you can learn how the core templates work by looking at this description and studying code inside the extension.
The TypoScript for the skins reside in files on the site's file sytem. If you do not want others to be able to read your TypoScript, you can prevent web browsers from accessing the files by using htaccess files or directives in apache config.