The built-in Telerik themes can only be applied to Telerik RadControls and a few MS basic controls, which are internally used by our controls for different purposes. Our theming mechanism is consctructed to work only with these controls and it is not capable to work with your custom controls. In our online documentation you will find more info about the Telerik themes and how to modify and apply them to the RadControls. I hope this information will help you. I believe that it will answer you to some of your further questions. As you might know with our latest Q2 release we introduces another theme - Metro which will be more appropriate in your case regaring to the modification:
"Metro UI for RadControls for Silverlight and WPF"
"Metro Theme Customization Made Easy"
If you need any further assistance do not hesitate to contact us!
the Telerik team
Register for the Q2 2011 What's New Webinar Week. Mark your calendar for the week starting July 18th and book your seat for a walk through of all the exciting stuff we will ship with the new release!