A few of my chicks "sat" in the bottom of the egg for awhile too, but they all made it out without help, just had to rest awhile and gear up for that final push. Ducklings and their eggs are bigger then the chicks though so if you think the heating element is a problem go ahead and help. I haven't hatched ducklings yet (11 under a broody hen and 9 more in the bator) so I'm not sure. If you do feel like you have to get into the bator I'd definetly go the hout steamy bathroom route so that you're less likely to jeprodize the yet to hatch ducklings.
ETA: It might be better to just slide the cartons over so that they're not under the heating element and not try to take the ducklings out. Prev. poster makes a very good point about the yolk sac possibly not being fully absorbed yet even though they're zipped.