In track advanced section you can select Adjust Spline height. Then just click on a spline and move mouse forward or backward to raise or lower spline height. Then you can select Smooth Spline Height and then left-click on a section of rail between splines and it will smooth the track and terrain between the two splines.
You can lay track over a hill and then use the above techniques to get nice cutouts in the hill with a much shallower grade.