This month the Vectorworks online User Group is looking at Stacked Layers/Unified View and how to set up your layer heights correctly. http://www.archoncad.co.nz/usergroup/join_int.php
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.
Stacked layers in Vectorworks 2008 and 2009 had some limitations:
you can't use Show/Snap/Modify others for the layer options,
all of the 2D tools don't work
You will find yourself turning stacked layers on, just for visualization. You will have to turn Stacked Layers off to work.
The Unified View in Vectorworks 2010 is a big improvement, you can edit everything, on all the layers.