Merging is (usually) easy. Solving the height difference problem is (usually) not. I note from your time line that you have the Android version of Trainz. So I do not know if the suggestion below will work or not.
If routes can be merged in Android, insert a number of new baseboards between the routes to be merged where you wish for them to be joined. The new boards will provide space to merge not only the track but the terrain, roads, scenery etc. Peter
