In the The Original Series
Pupils may have been the children wearing masks shaped like giant eyes in the audience. The masks might have been illusions created by the Eye, since they could blink like a real human eye.
In the Current Series
The masks often vary in size, shape, design, and color, so that the audience can easily tell them apart. They aren't always worn by the children, though. They are only worn by children in the audience. The children take turns sitting in the audience and starring on the show.