You can control the elevation of a massing model by setting the Z value in the Object Info palette. You can also use the Send to Surface command.
When you use Send to Surface command, Vectorworks will send the insertion point of your massing model to sit on the site model. The insertion point of your massing model is generally the corner of the polygon that you started first.
So, depending on where you started your massing model, your building will end up at different elevations. You might see a blue dot on your massing model when you select it in a Top/Plan view. Moving this blue dot has no effect on the Send to Surface command.