Ah, you have a NR360! Just fill both A and B wells, and don't worry what the number says. I use one for hatching, so I'm sure it will be fine!
What are the other eggs in there????
As far as a lone duckling, you have other older ducks, right? I would expect maybe 3-4 weeks (at most) and you should be able to introduce to your flock. Slowly and cautiously, of course. If you had a nice hen that may adopt the duckling, it would be nice. Or you may even consider separating the duckling with one of the adults first. Then let the adult introduce the little one to the rest of the group.
(p.s. I like to use a rubber shelf liner on the grate on the bottom of the incubator. It helps with them get better footing when they hatch (especially bantam chickens, which is the majority of my hatches), and it keeps the eggs from rolling around so drastically when they get bumped by others. Just a thought for you.)