5.2. The Special Case of the _layouts Folder
There is a set of pages to which the above service process does not apply. In fact, they are not held in the content database at all. These are the files that are served from the _layouts folder of a site. The _layouts folder is the location for various system pages, such as Site Settings, that access the administrative APIs, or perform other tasks at a very deep level in SharePoint. While most _layouts files are administrative in nature, and therefore not seen by a typical site user, there are some that may bleed through. The All Site Content Page (./_layouts/viewlsts.aspx) is a prime example.
The _layouts folder is a virtualization of a folder from the 12 Hive, typically C:\program files\common files\microsoft shared\web server extensions\12\template\layouts\. Every SharePoint site in the farm serves _layouts files directly from this physical path. Layouts files are not assembled from the database, and do not use the local site's Master Page (discussed below). This folder is read-only from the web sites, and does not appear in folder lists generated via the SharePoint Web API.
Because SharePoint Designer reads and saves SharePoint files via the Web API, you will notice that the _layouts folder does not appear when you open a site in SharePoint Designer. You are not able to access or make changes to _layouts files. This also means that most changes you make to an individual site will not be reflected in files served from the _layouts ...