We are not sure whether you are using project or assembly references.
Anyway, this issue is not particularly related to Telerik controls in any way, i.e. you would have exactly the same problem no matter what external third-party assemblies you are using -- our assemblies are not special in any way, i.e. they are just a bunch of normal DLL's -- nothing special.
The questions that you have are really Visual Studio and .NET material. Maybe, this MSDN topic can get you on the right track to resolve your assembly architecture. You can also get advice on StackOverflow for .NET-related issues like this one.
Let us know if you have any questions that are directly related to Telerik products.
the Telerik team