Stack two of the cups together, the open end facing up.
Put one ball inside the top cup, then, to hide the ball, stack the third cup over it.
Place the remaining three balls inside the top cup.
Drop the three balls onto a table, spacing them out in a row. Flip all of the cups over and place one behind each ball. Carefully place the cup with the hidden ball in the middle. Practice this maneuver to master it.
Set the middle ball on top of the cup behind it and stack the other cups on top. Magically wave your hands, then lift all three to reveal that the ball has "melted" through the cup. Remember that the middle cup now contains a hidden ball.
Space out the cups again, putting the middle cup, the one with the hidden ball, over the ball that's magically melted through. Again, practice this maneuver so you can perform it successfully. Your audience will now think that all balls are accounted for with two in a row on the table and one under the cup.
Place another ball from the row on top of that cup, then place the other two cups over it. Wave your hands again, then lift to show that now two balls are under the cup.
Separate the three cups again, placing the middle cup with the newly hidden ball over the two balls that the audience thinks have melted through.
Position the last ball on top of the cup with the balls underneath. Stack the other two cups on top. Wave your hands, lift the stack and reveal that the three balls have magically melted through.