Do you mean the Telerik.Web.UI or Designer.dll? The latter should be added into GAC on installation only and this is by design. In general, there is no need to add Telerik.Web.UI.dll into GAC explicitly.
The devs are working on the problem with the Prometheus designers in VS 2008. We will do our best to address all those for the Service Pack of Q3 2007.
As to the conflict, you may get that if you reference two different versions of a DLL within the same project/application. Otherwise, there should be no problem adding different dll versions into the GAC.
Please, excuse us for the inconvenience this is causing.
the Telerik team