In the VTK official wiki, there is an example of an application that opens multiple vtkRenderWindows. Did you have a look at it? Basically, that program creates a vector of vtkRenderWindowInteractor:
std::vector<vtkSmartPointer<vtkRenderWindowInteractor> > interactors;
and, at the end, it calls the Start() method on the last element of it:
interactors[3]->Start();
('3' because it opens 4 windows). Maybe you can adapt that logic to the application of yours...
Just as a final note, consider that - if you like - you can also have a single vtkRenderWindow with multiple viewports.