I recommend Scenery Builder (sb205) for both the roads and scenery mods. The roads are drawn as VTP lines, and depending on which VTP value you use (roads being usually VTP level 5 or 6), it might help to cut through any scenery where it doesn't show. If you use a VTP level similar to, or higher than, the roads that already exist, they will be displaced along the area where your new VTP line road is drawn. Sort of like beating it into submission.
I moved a river bank using the same program; you simply draw a new coastline on one side, make a water polygon to fit right up against it, draw the coastline on the other side and you're done. This same program also allows you to add numerous scenery objects including bridges. All in all it is very versatile.