This is quick tutorial on how to use my bricked-up viaducts to create junctions on elevated sections. This is how I do it, you may find a better way. One alternative is to construct it all at ground level and then just go over it setting all the spline point heights.
First add the Standard Viaduct sections where you want them.
Then add the standard track to make the junctions. I have changed the Viaducts to use the USA concrete sleeper track so I am using that same track to make the junction. To change the original viaduct change the bridgetrack entry in the config.txt file from 100395 to 101038. This seems to be the only other track which will work with these.
Now set the height of the splines, here I have used 8m for the height. As you can see, the joining track for the junction is now floating in the air.
Now add the "Diverge Viaduct" splines and adjust the height to the same value. Note there is an extra spline point in the one which is to be the curved section.
Now move the "Diverge Viaduct" splines under the track to fill the gap below the floating junction. Don't forget to hold the shift key down while you do it to stop them joining at the ends.
Add the point levers, and you now have your junction.