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I use them interchangeably. I have always used wait when we are going into or out of the house and I use wait when feeding them. During training and when doing the sit or downs, I use stay. They both mean the same thing and the dogs know what they mean.
At the star puppy class, Alli only knew wait at the time and the trainer didn't have a problem with which word I used. I have since taught her the stay command also.