Cloning EE sites

I am writing an application to ‘deploy’ EE sites, either using a ‘mastercopy’ as a template, or any other deployed EE site as a template. The goal being settings other than unique paths and urls will be preserved from the template to the new site. When a new site is deployed I create the necessary directory structures, copy necessary files, and create the database. I then duplicate the template sites database. Technically, all files / database are in order, and all I need to do is modify site specific values in the database and config.php file.

I am a little unclear on the relationship between the system/expressionengine/config/config.php file and the database. It seems that once a site is installed, changes to the config.php file are not reflected in the control panel (for example, I changed the site label and the documentation url). However if I modify the config file from the control panel config file editor, those changes are saved back to the config file.

Once a site is installed, what purpose does the config.php file serve? What variables in the config file are actually used when the control panel or site are accessed.

Any insight would be greatly appreciated.

Thanks