I would really like to hear the methods that people are using to clear and align energies and chakras.
It's common to do this from receiving healing. So for example, this is what takes place during transients' weekend healing sessions that I've been hosting for over five years. We just had a session before. This also takes place through things people wouldn't even consider, such as somatics; yoga, thai chi, qigong, Aikido, etc. Massage, energy healing, spiritual healing, Reiki, kinesiology, acupuncture, past life regression, equine therapy and so on.
Those that learn a form of energy healing such as Reiki, are sometimes taught to heal themselves first. For example, in Reiki a teacher may give an assignment to do self-healing for 30 days. Meaning placings hands on specific areas of the body, as taught in Reiki for self-healing. This clears, aligns, balances and unblocks the energy system.
The most efficient method of self-energy-work, that really relates to what you asked, is what Sinera mentioned. Robert Bruce's book, Energy Work, is really the best out there to learn how to work with your energy. It doesn't just cover the chakras, but all the minor energy centers, and does have mention of the central energy channels. He teaches methods for storing energy as well for later use.
Through doing that, which I did consistently for a few years, about a decade ago now, you begin to develop psychic senses to help you understand what areas of your energy system need the most work. Also through doing this, latent psychic abilities come out, and new ones can develop. If you are a person that is into astral projection, energy work will help with that as well. There are specific techniques you learn to use before using a projection technique to get out of body.
When I do a healing, if I take the time to do so, I can scan each energy center and pick up on what needs the most attention through physical sensations in my my hands. I then use various techniques involving different colors through visualizations to balance, align, clear and strengthen said centers. I would then scan after the healing and notice a change. (I was taught this within a 1.5 year diploma in energetic healing in Australia) It's a lot more advanced in my oppinion, than Reiki (I'm a Reiki Master).
You may be aware of the book
Hands of Light by Barbara Anne Brennan. This is one of the best resources as a healer, if you are looking for information on healing another person.
I'm also trained in crystal healing, where I use specific crystal layouts on the body, in addition to a pendulum, to perform the healing. This again will help balance, align, clear, etc.
I always come back to the self energy work as the best method for working on self, as you don't need anything. We are each powerful beings, so while we learn about different tools we use, such as crystal wands, all we really need is out mind and thoughts. But something important to remember is that we still need to address the emotional links for some blocks, as no matter how much work we do, they will remain unless we get the memory to appear through something like past life regression. This is not always the case. An example: earlier on this year I did a distant healing and cured a bakers cyst on a friends knee through energy healing (I don't use Reiki anymore, unless someone asks specifically, as I find it limiting and some people don't want to be touched)—she didn't need to address the emotional link, but it's possible she had already understood it, but just needed some help to shift the energy on.