1. He is moving in the seat.

2. He is moving on the seat.
3. He is moving at the seat.
[Which prepositions can we use? Are the three have the same meaning? Which one is commonly used?]

If he's wiggling around, then you'd most likely use "in" or "on." I can't think of any circumstance when you'd use "at."

Remember, "in" usually means "inside" and "on" usually means "onto" or "on the top of."