Can u tell me the functions of the red, black and yellow wires? I have changed the control box but do not know where the ground should go.

There are 2-wire and 3-wire well pumps. Apparently you have a 3-wire pump. The 2-wire pumps have a starting relay build into the pump. The 3-wire pumps are capacitor start motors and have a capacitor and starting relay in the control box. The yellow would be the neutral, (or common if 240) red and black would be the start and run circuits.
Does the well wire have a ground wire? I believe most present day well wire has a ground. I don't believe that has all ways been the case. If your well wire cable has a ground connect your ground to it and the box. If you have no ground wire in the well cable, which is probably the case or you wouldn't be asking the question, just connect the ground to the box.