Chakras rotate clockwise and anti-clockwise simultaneously. Clockwise rotation absorbs energy, while counter-clockwise rotation projects or expels energy. It is normal for a chakra to do both at once.
When deliberately trying to energize or absorb energy you can facilitate the rotation of the chakras by rotating your hands, or by just willing the chakras to rotate. I am referring to the hand minor chakras.
The other major chakras are capable of projecting and absorbing energy. It is generally a bad idea to use your own crown, ajna or throat chakras on another human being. Lower clairvoyant senses and simple etheric projections start from the solar plexus. Be conscious of reabsorbing the energy when you are done with them. The safest way of transferring energy between humans is through the hand minor chakras. You can use your hand chakras to clean and energize the diseased chakras and energies of another human being.
As your chakras become more active during meditation, the rate of rotation increases. Size may also increase. There is no need to control the rotation or absorption itself, but holistically, you will want to develop balance among all the chakras, meaning keeping them all in proportionate size and making sure one does not dominate over the rest, or that any one of them becomes under-activated. This takes more than just meditations, but careful attention over every aspect of life.
Are you aware of the physical, psychological and spiritual functions of the chakras? Understanding of these factors is what will allow you to achieve balance, not manipulation of the individual chakras - which is done mostly in the treatment of physical and psychological diseases. Several books have been written on the subject.