The XML descriptors are only used for initial configuration or reset of Portal's data. They are not updated by Portal to mirror the current state of your Portal. Please take a look at the reference guide for more information.
When you add portlets, you need to also supply a portlet-instances.xml file and *-object.xml file, or else they will not appear. (Well, you could go into them anagement portlet and add them theree.) Information about these files, and how to use the management portlet, is also in the reference guide that Chris mentioned.