The layout uses a state-of-the-art configuration known as a "mushroom".
Below are two detailed trackplans showing the two decks of my HO Siskiyou Line layout (one plan for each deck). This particular deck configuration is known as a "mushroom", because the two decks face in opposite directions.
This is the track plan for the upper deck of the Siskiyou Line. To see a larger view of the upper deck track plan, just click on it.

The upper deck is typically viewed from a raised floor (15" in this case), so the upper and lower decks appear to be close to the same relative height off the floor (see the cutaway diagram, below). This track plan is the latest plan, updated to be current as of 2005. We use this track plan in the Siskiyou Line video series to discuss various parts of the layout.

This is the track plan for the lower deck of the Siskiyou Line. To see a larger view of the lower deck track plan, just click on it.
This is a cutaway view of the layout at section A-A on the plans. This clearly shows the "mushroom" configuration, with the upper and lower decks in the middle that face opposite directions, and the 15" raised floor for more optimum viewing of the upper deck.
For more information about doing mushroom designs, see my articles on mushroom design in the January and February 1997 issues of Model Railroader magazine.