I guess there are many ways to meditate with crystals, but there are some basic things that everybody likes to go by and this is the way that I use and like best.
There are the 7 basic chakras shown in the picture above (actually there are more, but 7 main ones) kind of energy centers in your body. Well, they have colors associated with them too. An easy rule is to pick a stone the same color as the chakra for that chakra, although there is always some unusual ones that are different. And you can't mess up! Its not like something bad will happen and the universe will implode if you use a throat chakra stone on you solar plexus chakra!
The first or "base chakra", located at the very base of your spine, is about wanting to exist in the physical world, survival, passion for life. Some stones for it would be rough ruby, fire quartz or garnet, red jasper.
The second chakra, sometimes known at the "tribal" or "sexual" chakra, is located in your pelvis just above your pubic bone. Its color is orange and this chakra is all about relationships, connections, and again intensity. Some good stones would be carnelian or tangerine quartz.
The third chakra, the "solar plexus" is located between your ribcage and your navel. It is about our sense of self or ego (not in a bad way) in the physical world. It is associated with the color yellow and some stones would be citrine or topaz.
The fourth chakra (my personal favorite!!) is the "heart chakra" located in the center of the sternum (breastbone). This one is all about emotions and sadly it is where much emotional pain can accumulate. Now this one is different in that there are TWO colors associated with it--pink and green. This means there are a ton of stones for the heart chakra...rose quartz, jade, rhodochrosite, chrysoprase and pink kunzite, just to name a few!
The fifth chakra is the "throat chakra" located at the base of the neck. It is all about expression of course (not just speaking your truth, but living your truth, manifesting your truth, etc). Its color is blue. Some stones would be aquamarine and aqua aura quartz.
The sixth chakra is called the "third eye", located in the middle of the forehead just above the brow line. This chakra is all about your innate ability to see and perceive beyond what is in this world! And here the color system breaks down a bit. an indigo stone such as iolite is a good choice, but there are many others good for the third eye-herkimer diamond is a nice one! Apophyllite is also a good one!
The crown chakra is focused actually several inches up off the top of your head (at least for meditation purposes, the way I've been taught). It is a gateway to all of the chakras in your body and is associated with the color white! Quartz crystal is an excellent choice for this chakra as is amethyst or phenacite.
Now, when you meditate whith stones, you need one stone for each chakra, a grounding stone at your feet and two pointed crystals to hold in your hands (like nice sized quartz crystals or whatever you are drawn to).
The idea of grounding is that it drains any excess energy from us that we do not want there, kind of a negativity vacuum. Good grounding stones are Howlite, hematite, pyrite, apache tear and black tourmaline.
You proceed to lie down flat on your bed or a mat with a pillow for your head, a blankie near you in case you get cold, and your stones in a pile in your hand or within reach.
You begin by placing the grounding stone about 6-12 inches down from your feet. Then you lay the red stone on the base chakra, the orange stone of the pelvic chakra and so on up until you are lying flat reaching up over your head to set the crown chakra stone in place 6-12 inches above your head. Now you have all your stones in place--be still all they will wobble off! Take your two larger quartz crystals. Place one with the point touching the palm of your left hand and place the other with the point facing out in your right hand (arms should be resting out at your sides with the crystals in them).
Basically, once you do this you can then use whatever meditation technique works best for you. I like to deep breath imagining that I'm getting rid of everything that feels negative in waves going down to the grounding stone as I exhale. I do that for awhile until I feel a difference. then I focus on each chakra and the stone there starting at the base and going up, trying to build the energy there. When I get to the crown chakra, i imagine mine open with white light from the universe, god, whatever you wish to call it streaming in. Then I focus upon my hands. The left hand if for receiving the energy of the stone, so I just focus on letting that in. Then the right hand is for manifesting in this world what you want, kind of like holding a wand! That part is fun! I focus on everything i wish to create and manifest in this life (which has a much higher probablility of manifesting, when you are in a deep meditative state like that)! Then I just get quiet and try to still all thoughts so that anything can come in that I am meant to hear.
Best of luck from Puppy and me on your journey exploring meditation! It has become challenging for many of us to become still in this sometimes frantic world. However the benefits are immense! If you are a concrete thinker who wants to stick with the proven, there are numerous studies which conclude that meditation improves quality of live and reduces stress related illnesses. For those willing to consider the more abstract, it is said that regular meditation helps us to "raise our vibration", which essentially means make spiritual progress during our physical incarnation. People report seeing clearly on a creative and intuitive level during meditation. It is a worthwhile practice that crystals can enhance!