So you are trying to model a watercourse (stream/creek/brook/river) in an arid [desert] area, and are you trying to model where the watercourse's liquid disappears and reappears but the terrain it still indicative of a watercourse?
My interpretation of what you posted is that you have a Digital Elevation Map (DEM) of the area which you have used Transdem to create a route map in Trainz and are trying to model the fine watercourse features of a desert. Based on that, it seems like you want to be able to put in a spline under the terrain that can then be referenced to bulk update so that you aren't spending weeks modeling thousands of miles of streambed.
If I'm somewhat correct, I've no idea if it is even possible, and suspect that it isn't. It has been years since I messed with DEMs, but as I recall you get the TIGER data overlaid as a graphic/ground texture.