This is the overall layout design I am using. 
The black track is the lower level and is basically flat. The magenta track is the connection between the lower and upper level track. I call it the Mid-Level. The blue track is the double track upper level and varies between 10.75" and 13.29" above the framing. The red track are custom cut sections of track.
The following three drawings shown each of the three levels separately.
I used the CAD program to design my layout because I wanted to be able to get coordinates for any point on the layout and be able to translate that to the actual layout. On the bottom left of the drawing for the Upper Level 0,0 of the coordinate system is called out. I marked out a grid system on the framing from which to measure and locate any point.
I am a retired structural engineer whose area of practice was highway structures like bridges, retaining walls, etc. We used stationing along the alignments which were also the profile grade line. I used that same system for designing my layout. On each level drawing you will see Stations, Elevation, and in some cases coordinates for points along the track.
