Thanks for your reply peter. The problem with using the method that you suggested is now the NavigateUrl in the Template no longer points to the correct location. I tried using NavigateUrl="~/MyRootPage.aspx" but still get an error.
To re-cap:
I have my OfficeTemplate file in the root of the application.
On the menu, I have a RibbonButton that has a NavigateUrl="MyRootPage.aspx"
I have a page in the root folder called "MyRootPage.aspx" which uses the OfficeTemplate. When I compile and run, the RibbonButton loads the proper file.
One page that also uses the OfficeTemplate is located in a subfolder /Folder1/MySubPage.aspx.
Based on your previous suggestion, I add the clientscriptblock code to the codebehind in the "MyRootPage.aspx" and /Subfolder/"MySubPage.aspx" so the JavaScript files would load properly. Now when I click on the RibbonButton from the "MySubPage.aspx", it can no longer find "MyRootPage.aspx" becuase it is looking in it's current folder.
If I change the NavigateUrl to NavigateUrl="~/MyRootPage.aspx" that also causes the "resource cannot be found" error.