When the justice meter is full, and you have found the appropriate runestone, any equipped weapon needed for the runestone attack will glow based on the elemental type.
You must press both of the weapon buttons at the same time to perform the attack. e.g. for the "Flaming Blade" attack a spinning blade and a fire axe must be set as active weapons then the two buttons are pressed at the same time (e.g. buttons A and X). Remember that the justice meter must be full to be able to use the special attack.