Incorporating crystals into your meditation is a creative (and intuitive) process. You can hold them, of course, or wear them as jewelry. There are resources that explain how to place them at certain points on or around your body for particular purposes (see the entries on chakras for more detail). I like to contemplate mine by candlelight, turning it in my hands.

Healing with Crystals and Chakra Energies by Sue and Simon Lilly offers a number of crystal-, color-, and chakra-based meditations for all levels. For example, one method promotes the flow of energy: you hold a clear quartz crystal in your non-dominant hand with the tip pointed toward you, while holding another clear quartz in your dominant hand with the tip pointing away from you.

Healing With Crystals and Chakra Energies

It is important to realize that in physics today, we have no knowledge what energy is.