There are two ways in which to provide a new color scheme and layout for an organization:
Define a new set of templates - You can define a new set of templates in PortalServer-DataDir/portals/portal-ID/desktop/new/ and make this directory (new) the Desktop Type attribute for that organization.
Define a new theme - In the display profile, you can define your own theme in the GlobalThemes collection. See Chapter 10, Customizing the Global Themes for more information.