The plugs are there to help you regulate oxygen levels (which the chicks/ducks need) and humidity. Plugs in=higher humidity, lower oxygen. Plugs out=lower humidity, higher oxygen.
Basically, you'll have to decide this for yourself, because it varies by situation, and that is why you will hear differing opinions. If your humidity is too low toward the end, you will have serious hatch problems--your babies will stick to the shell and the membrane will dry out and they won't be able to escape. One way to raise humidity, is to put in one or both plugs. Unfortunately, that also reduces oxygen, which the babies have a higher need for at the end of the hatch.
Personally, I leave mine open at the end. They need the air, and the only way to get air is with open plugs. But there is another way to get humidity--add more water evaporation surfaces. You can fill the evaporation pans. If you still don't have enough humidity, you can put damp sponges in the bator. If you've done that as well, and are still having trouble, THEN you might want to consider covering one of the holes--but never both. The chicks MUST breathe--that is even more critical than humidity.
Unless you live in an extremely dry climate, you shouldn't have trouble getting the humidity up using the methods described. Just be careful not to get it TOO high--that causes problems too, because the water condenses on the inside of the shell and can drown the babies as they pip.
Sounds complicated, but it's really not. Good luck!
(Edited for clarity--I had said "remove both plugs" where I meant "put in one or both plugs."