Hi Ryan,
I am not sure if I understand your scenario completely, however, in general the RadWindowManager has the getWindowByName(), getActiveWindow(), getWindowById() methods that help getting a reference to the desired RadWindow.
I hope this information helps. If you still experience problems, please open a support ticket and send me a sample project that shows your implementation and the problem itself. I will check it and get back to you.
Sincerely yours,
Georgi Tunev
the Telerik team