Right now is day 18 of incubation I am a bit concerned. I have the eggs in cartons right now but I am not sure if I should keep them in cartons or put them on their sides.
People do it both ways. You'll find some people that very strongly believe that the cartons are the only way to go, and you'll find some people that believe flat is best. I consider it a personal choice issue, do whichever makes you happy.
The recommendations that came with my incubator say to lay them flat, so that is what I do. The way I look at it, the incubator manufacturer wants you to have success so you'll buy or recommend his product. But I think they are just giving you a simple way that works so they don't have to explain as much. I believe the egg carton method works equally well. But if you go that way, it is probably a good idea to cut the bottoms out to give good air circulation.
Also, I have some left over duck starter (actually alot of it!) could I feed chicks that? Because I am only doing chicks this time then going back to ducks so I dont feel the need to buy a huge bag of chick starter since I give them back to the farmer in a week anyways..
I don't do ducks and don't know what duck starter you have. Unless there is something really weird about it, I'd expect it to be fine for a week as long as it is under 30% protein. People get hung up on feed, but when a broody raises chicks, she does not monitor their exact feed intake that closely. A wide range will work, especially since it is only for a week.
When I hatch turkeys with my chicks, I feed 24% game bird starter to them all. With chicks I hatch, I've not had a problem with pasty butt. With shipped chicks, I have had some problems. I think it is more due to the shipping stress than the feed, but that is just my opinion.