I have done both.
I did not see an increase in % hatch. I did see the chicks zipping and kicking out of the egg shells easier. The incubator was a lot less messy.
On the downside, I had more holes (cups) then eggs, and two chicks 'rested' in empty holes with a leg hanging over the edge. We have had to rubberband hobble their legs together. They are walking better, but the leg seems to be 'sprung' at the hip.
Also, one of the cartons wicked water up from the tray below. I don't know if it made any difference, the eggs hatched but I did remove them from the carton.
If we do it again, there will be no extra holes.
We are going to discuss whether we do the egg carton thing again. I am leaning towards not. I have to clean the incubator anyway. And the chicks with the hurt legs makes me sad. Hopefully they will recover.