In Rise of the Empire during the level Felucia - Heart of Darkness, the easiest way to kill Acklay as a clone is to get in a high place where the Acklay can't reach you, and proceed to shoot them. The Blaster Rifle and the Blast Cannon are extremely effective at destroying them, as are the Elite Rifle and Flechette Shotgun. Alternately, you can also use Mines or Rocket Launchers to kill them. Thermal Detonators work great too. But, if time permits, you can become a hero and use your Lightsaber. It is advised to not approach and attack the Acklay directly, but rather use Aayla Secura and attack with her Saber Throw.