I don't know that there is any real difference in hatching them upright, like the egg carton method, or laying them flat. You'll find different people doing either and convinced their way is the best. I really think a lot of it is personal preference. I lay them flat, but as far as I am concerned, that is not the right way or the wrong way. It is just my way.
One reason I would suggest you not use the turner is that the chicks make a mess when they hatch. You really need to clean pretty well when hatch is over. Depending on what your turner looks like, the electronic parts could be hard to clean without getting them wet.
I have not used the turner during hatch so I don't know how big a concern this really is, but my turner has several places a chick could get a foot trapped.