I suppose it could, but you run the risk of the yolk becoming stuck to the side of the shell.
You can incubate them in a standing position - that's the premise behind automatic egg turners. If you don't have an auto turner, you can make a turner out of an egg carton. Cut the top off of the carton, punch a hole in the bottom of each cup to allow the cup to drain in case water gets in, and place the eggs pointy end down in the egg cups. Place something under one side of the egg carton so it will tilt to one side. At least once during the day, move the wedge so the egg carton will tilt towards the opposite direction.
Now, if you decide not to do the egg carton approach (which most of the time results in a higher hatch rate), you can lay them down flat in the bottom of the incubator. Place an "X" and an "O" on opposite sides of the egg and hand turn them at least twice a day, with 3-4 times being ideal.