Create maps constantly to show yourself your ongoing work in macro scale. You can also edit a map in an art program to draw in the base of a feature, then open that in the terrain editor and use it to guide painting that base in by hand. Then create a map so it shows what you painted in. Then pull your feature up out of the painted area with the raise hill or bulldozer tools. That will also take care of about 50% of your actual painting of that feature if you use the right tile for your 2D painting of the base area.
You can see these techniques in my ongoing posts documenting the terrain I'm currently building. Also check the one concerning making mountains to see an issue you will always be faced with because of the polygon mesh the 3D structure is formed by. Even if you use Artik's topographical import program and create a hieghtmap file for the terrain editor, the polygon mesh will still effect the structures. It is very hard to get away from having to visit every square mile of your terrain looking for polygon mesh issues. This is one of the first things you will run up against once you start shaping features with any elevation to them.