Generally when I do chakra meditation I prefer to do it while standing.
I'll often first focus on feeling the bones of my body, working from the ground up, and then I focus on the chakras.
Depending on the day and my mood I may focus on the chakras in addition to the organs and the meridians, or I'll just focus on the chakras.
While the chakras do have specific qualities associated with them, here I'll focus on helping you to focus on their location. While you might choose to focus on feeling a glowing wheel or ball of energy, I find that I sometimes get a better feeling when I focus on pin point locations within my body.
And as I do my chakra meditation, even though I'm focusing on specific chakras I also stay aware of the rest of my body so that I can maintain a comfortable upright posture. It's as if by meditating on the chakras I affect my posture and make it more comfortable to stand straighter and taller. It is as if I am tuning my body with just the right amount of tension in all of the parts.
Often times when I meditate on the chakras I start of with the "general location" of the chakra and then try to move my awareness aroudn that spot until I fine tune the location of the chakra.
For this it's helpful to have a general awareness of where the bones and joints of your body are so that you can use them as references.
How long should you focus on each chakra? If you've had a reiki session and you've been told that a particular chakra or set of chakras are weak then you might want to focus on those chakra's a bit longer. I'd suggest go by what feels right. If you are new to meditating and get tired or bored easily, then spend a few breaths on each chakra and then rest. And then as you get more used to meditating, work at extending the time.
You might find that it feels good to focus on one chakra, or you may find that you just want to do a quick scan and get on with your day. Do what feels good, do what feels right.
And if you want to push yourself to meditate longer, then work at refining your awareness or on focusing on the chakras in different ways. Basically what I'm saying is occupy your mind in different ways to help you meditate on your chakras (and other energy structures) in different ways.
While actually doing a chakra meditation you can imagine breathing into the spot you are focusing on. Or hold you awareness on your chosen chakra while keeping your breath slow and smooth.
Generally when I do a chakra mediation I start from the ground up but you might experiment with different sequencings of your chakra meditations.
For the root chakra meditation you can start at the tip of your tailbone. From there you can move your awareness forwards just a touch to a point just in front of your anus.
While you are focused on this point you might first want to focus on your feet, shins, knees and thighs. Make adjustments so that your weight is even through forefeet and heels and from side to side. You might also want to adjut the rotation of our shins. First make sure both shins are even, then try sliglty inward or outward rotating so that feet, shins and knees are comfortable.
For the sacrul chakra meditation start of by focusing on the sacrum and then move your awareness to the top of the sacrum.
With your imagination, draw a line from the top of the sacrum to the belly. (For me this line ends midway up between pubic bone and belly button.) Next draw a line from hip joint to hip joint. (The greater trochanter is the part of the thigh you can feel at the top of your thigh. the hip joint is actually a little bit higher than this.)
Focus on the point where these two lines meet.
As you focus on this point you might want to tilt your pelvis slightly forwards or backwards. Find a position where you lower back feels open…. full.
I'd suggest that the solar plexus chakra is at the level of the bottom of the back of your ribcage. At the front of the body this point is above the belly button but below the bottom of the sternum.
Focus on the midline of your body (from front to back) and move your awarness up or down between the height of the belly button and the sternum.
You may find it helpful to focus on the bottom of the kidneys and then move your awareness forwards (slightly) from there.
While doing your sacral plexus chakra meditation, you can also focus on feeling the bottom part of the back of your ribcage (the lowest 2 or 3 ribs.)
For the heart chakra meditation focus on the base of the heart, the roof of the diaphragm.
Failing that, focus on a point behind the bottom of the sternum.
Move your awareness so that you are focused about midway between the front and back of your body.
While focused on the heart chakra you may find it helpful to adjust the front and back of your upper ribcage. Try bending your upper ribcage a tiny amount forward and open the back of your ribcage as well as the front. If this causes your head to go forwards alot, then pull your head back while trying to keep the upper back part of your ribcage feeling "open".
For the throat chakra meditation focus on a point just below the bottom of the adam's apple but above the top of the sternum where the collar bones connect.
while focused on the throat chakra you can adjust your head so that your neck feels long but also adjust the hang of your arms by widening the bottom tips of your shoulder blades. See if you can make your upper back and the front of your shoulders both feel open. Widen your shoulder blades first to widen the back and then roll the fronts of your upper arms bones outwards to open the fronts of the shoulders.
For the third eye chakra you can focus on the point at the middle of your brow (on the ridge of bone). From that point move your awareness inwards to about the depth of an eyeball.
Try to relax your brow and your eyes when focus on this point. For that matter relax your face as well.
When I first learned about the crown chakra I thought it was at the crown of the head and this may be true for you. You can focus on the exact top of your head. Of you can try moving your awareness down from there to a point miday between the top of the head and the back.
You can imagine the crown chakra being at the root of a high pony tail.
While focused on this chakra you can focus on making your spine feel long, from tail bone to crown chakra.
A final closing for your chakra meditation is to scan up and down the chakras. Inhale up and then exhale and relax. As you inhale mentally touch each chakra one by one. And then relax your awareness (and your body) as you exhale.