Rhino panel configuration information is stored in the “HKEY_CURRENT_USER\Software\McNeel\Rhinoceros\5.0x64\Scheme: Default\DockBarTabs” key located in the Windows registry for version 5.0. The key contains collections of visible panels and is written as part of the Rhino shutdown process. When Rhino starts it looks for this key, if the key is not found then the default Rhino panel configuration is displayed.
If you were to arrange the panels in the configuration you like, close Rhino then export the registry key you would have a REG file containing this configuration. You should be able to restore it by deleting the key then importing the saved key then starting Rhino.