Being set mostly on a hillside, we had this problem everywhere on the DHR.  What we did was to let the higher track set the terrain.  Wherever it hid the lower track, we went into the terrain tools (topmost pop-out), minimized the activity circle and chose the right-top icon (the one that lets you drag the mouse back and forth while holding the LMB to raise and lower terrain).  Being very careful, it is possible to lower one edge of a square of terrain without disturbing the other edge.  This way, you can lower the terrain so you can see the lower track.  This works even better if you've made the terrain into 5M squares instead of 10.  It is tedious, but does make things look nice.
Occasionally, we'd have to stuff a bush or something to hide an unsightly gap.
Bill