When you are logged in with admin rights you can setup templates and page layout configuration. Page layout is stored inside "include/ inc_conf/ conf.pagelayout.inc.php" every time you made a change. That's why you need write access to the file. Page layout configuration is planned to be extended in the way that every template can have its own page layout and is stored in database.
Specified values are used to render the base table when the frontend (index.php) is loaded. On the picture you can see how every "block" is predefined. It orients itself on general website layout but with flexibility to hide blocks if not sepcified (e.g. width or height is set to zero or nothing). Parallel to base table definition main page properties like margins, background color or JavaScript onLoad can be made.