I also am curious about customizing the classes and layers of Vectorworks Architect. My firm uses two different CAD programs and would like the file structures to be similar. We are trying to set up our office CAD standards. We are all relatively new to Vectorworks, so everything is an experiment. We've tried renaming the classes as defined by the Set-up Assistant, but this inhibits the use of the Task Manager, and most likely changes relationships between classes/layers/sheets. We need to be able to add sheet types such as lower and upper slab/trough plans as well as add classes and layers that are specific to our work with sound studios.
Your office has gotten further in your experiments than we have, so I look forward to whatever replies are made to your topic.