Folks have been talking about using different kinds of scuppers in their skiffs and finding that they all leak. I did mine the way Renn suggested and found that it works pretty well. He says to put a tube in the transom and make what's called a stinger for it. This is a 2ft, piece of cloth (he suggests backpack, waterproof cloth) that is glued together and slipped on, over the tube. You put a line in the end and simply pull it up to close the scuppers. When you need to open them, just release the line and the cloth tube drops down into the water and any water in the boat that needs to drain out does but very little water comes back in the boat.
I added one little touch. Since I used 3in. drains I was able to go to my hardware store and get plumbing stoppers for 3in. pipe. These fit right inside the tube from inside the boat and make great plugs. They cost less than $2 each. There were some nylon ones that I could have ordered and then I would not have to worry about rust but for $2 and a little silicone spray, what I've got has worked well for 3 summers now. I'll try to add a photo of the stingers later. I found that you do need to make them at least 2 feet long or you'll get wave action into the top when they are up and that water will drain into the boat. Notice in the photo that the pvc is roughed up quite a bit where they are glued in to the boat to give the epoxy some teeth to help hold them in place.