If you deploy the masterpage as part as an feature (SharePoint solution) with for example Visual Studio 2010, the MasterPage will be deployed to the features directory. The feature file will provision the masterpage to the MasterPage Gallery (_Catalogs). As long as the file is not customized by SharePoint Designer, sharepoint will serve the masterpage (by using the virtual path provider) from the filesystem and not from the database.
<File Path="MasterPageModule\abc.master" Url="_catalogs/masterpage/abc.master" Type="GhostableInLibrary" />
Deploy the master page. You can now control the master page by changing it from its physical location (SharePoint Root - 14 folder) and still be able to access from /_catalogs/masterpage/abc.master
The above is the recommended approach when you deploy master pages and page layouts.