Don't forget the handy webcam for those comfortable with it.

One of the more memorable punishments was for a sub that wasn't showing the respect I wanted. She had to kneel facing the wall for a while with the cam trained on her. I was really proud of her for doing it and sticking with it. Watching her was quite the experience as well.

As for setup and making sure they know they are punished. Same as you would in real life. Talk with them so they know why and make sure they know they are being punished.