I would lay them down flat to hatch. I bought 16 bantam eggs almost three weeks ago. Candling showed that most have a saddled air cell. Eleven have made it to hatch-almost-which is Saturday-and they are under a broody hen to hatch lying down, of course. I have done this before successfully with duck eggs.
Come hatch day, be prepared to assist hatching with some. Eggs with a damaged air cell also mean the chick/duckling may be positioned wrong in the eggs preventing it from hatching normally. Assisted hatches are not that hard, but if you have never done it before I would urge you to research this now and be prepared; hopefully, the ducklings won't need help. I have five wonderful call ducks; without assisted hatch I would only have three.