After your chakra stones have been cleansed and charged, you have to activate them to suit your needs. If you are using crystals for yourself, you can program them for specific needs. If you use the chakra stones for healing on other people, it is best to program them only for basic healing and not for some specific tasks.
Before you begin activating your crystals, find a quiet and secure place and relax. Take the crystal in your hand and try to feel its energy. Imagine the white light coming from the universe shining all around you and inside your body, connecting you and the crystal. In your mind or out-loud state your purpose and intention to the crystal.
In case you use crystals for healing, you can form your intention in the following way: "Please allow me to use your energy in the best interest and intention to heal my friends. Please balance the energy of the people by whom you will be utilized and help them heal physically, mentally, spiritually and on all other energy levels."
If you are programming the crystals for your personal healing, you can program different gemstones for different purposes. Let's say you have problems with stability and security in life. You probably need to work on your root chakra (Muladhara). In this case, you would choose crystals like Hematite or Red Jasper, which work best for balancing the grounding energies of the first chakra. You could program them with the following intention: "Please help me gain more stability and security in my life situation, heal my connection with the Earth and help me ground and deeply root myself in order to reach stability and calmness in my life."
When you are making a statement and expressing your intention, you can also ask for the help of other things (energies, spirits, elementals, saints) which are close to you. For example: "Please, spirits of the Earth, enter this crystal and help me gain more stability," or "Jesus and Mary, please bless this stone to protect me from all negative influence of other people," etc.
Each crystal has a particular function but you can also program it with different intentions. You can use the programmed crystals for meditation and healing, or you can carry them as amulets for protection.