Holystoning was a job that could be used to make work if the mates thought the crew were having too much leisure. It was decidely unpopular. There seem to have been several ways of doing it. Some mention large stones being dragged over the deck on ropes. More often it was done by the crew getting down on their knees and scrubbing the stones back and forth. In this attitude, they appeared to be looking at the stones and saying their prayers. Hence holystones. I think this is more likely than the claim that the stones were originally tombstones stolen from churchyards.
The mates commonly told the men to leave no holidays, holidays being areas missed by the stones.
On the Queen Mary, the process had evolved to a point in which the stone (about the size of a shoe box) was placed in a metal clamp at the end of a mop handle and the decks dressed by a work party of about a dozen.