At some point Stormy mentioned an underground view showing the tube system. There's your answer. The tubes are shown in the underground view, and the walls are shown on the surface. No big deal about where the earthworker builds, or having the tubes go through the walls - they go under it.
My question for Stormy is, if there is an underground view for tubes, how do we go about building tubes? Perhaps instead of building the tubes tile by tile, tell the Earthworker "connect X structure to Y structure with tubes" and it digs a really deep ditch in a straight line (unless there is obstructions, in which case it goes around) between the structures, and then sets the tubes in, and then buries them? And if a tube connection already exists it says "thats already connected, moron" or something to that effect.