After cleansing the stone or stones, it is recommended to set the intentions of specific stones for how to plan to purpose them. If you are leaving the stones open to just flow energy then this is not required. However setting an intention gives a stone a purpose, which is more effective when the stone has been cleansed and also when the intention is specific and clearly projected.
Programming of the stone or crystal is done by holding a cleansed crystal in your hands, or holding it against the most corresponding Chakra. With closed eyes, and deep breaths, going into a trance like meditation, focus and project your intentions into the Crystal either verbally or silent. Making sure that the intentions and thoughts are positive, and some people visualise and surround the crystal is white positive light and energy before projecting the intention.