Here is a picture of a supercedure cell (middle of frame) from the bee course
here at beemaster.
And here are some swarm cells (bottom of frame).
Hopefully these will help you determine if you saw queen cells or not. Don't be confused by smaller, half height vertical cells that they tend to build alon the bottoms of frames. If you see what you think is a queen cell and it is not sealed, take a peek inside. If it is a queen cell you will see a good amount of royal jelly (white cream).
I don't like keeping queens from supercedure or emergency queen cells because there is a higher chance they will be inferior. I always requeen with a quality queen.
If you are in the process of supercedure/emergency, wait until you are certain there is not a replacement queen around before you attempt to requeen. If you introduce a new queen, and there is a virgin queen in the hive, the bees will kill your new queen. So wait until either the virgin queen mates and starts laying or until you are certain that the attempt at rearing a new queen had failed.