Stacked layers was a new technique introduced in Vectorworks 2008. Before Vectorworks 2008, if you wanted to see a complete view of your project, you would make a new layer for 3D viewing. Then you could layer link all your design layers to the 3D model layer. In order to view your model, you would change to this layer and make all the Layer Options Active Only. This would be the place to set up views for rendering, creating elevations and so on.
With Vectorworks 2008 and 2009, you do not have to set up the 3D model layer. Stacked Layers allow you to see all the visible layers in your file, and when you move the view around, all the layers look like they are joined together. Vectorworks uses the layer Z height to get all the layers to set correctly in 3D.