The repeating chemical structure of crystals is said to invest them with a kind of memory. This means that crystals have the power to hold energies.
You may hold a quartz crystal with the intention of filling it with your love. This is what is meant by programming a crystal. All you need is intention and focus. The crystal will remember your love, which will then permeate any environment in which the crystal is placed.
Crystals can remember negative as well as positive energies and so will sometimes need to be cleansed.