You don't need to fill it up with more sand to get the Shadow Ball TM.
Well, technically you don't have to. You have to get to the point in the game's storyline where you must go to the Relic Castle (A little before the final gym). Upon entering there, you are granted access to the higher floor of the castle, which will transport you down as you strategically maneuver between floors through the use of the quicksand pits.
Along the way, you'll just happen to find the TM chillin' on the ground. After you beat a couple Plasma grunts, you can continue your way to collecting it.
