Here is the finalized version of the 2009 xmas tree layout using an MTH Premier R40 Subway set, Lionel Fastrack, MTH Graduated Trestle System, and MTH Realtrax Trestle Set.
Here you can see how close the train is to the upper deck when it has to go under.
Here is the upper deck view of the spiral.
And here is the lower deck vantage point.
This was the 1st version, but due to the incline of the spiral it's better to have the train go down on the steep grade.