Sigh… where do I begin with this one?
Firstly, the medicine that comes out of China has no concept of chakras, especially in relationship to acupuncture theory. Chinese medicine is of Taoist origin, not Vedic origin. So simply said, there is no theory of needling or manipulating chakras based on traditional Chinese medical thought (I will address marma-puncture at the end).
“But my acupuncturist needles my chakras and it makes me feel terrific.”
I don’t want to take away from you experience and if you find benefit from whatever your acupuncturist is doing then keep doing it. However, you are not receiving acupuncture; you are receiving some new-aged version of acupuncture where there is no objective basis for your treatment plan. If you are trying to help a disease using acupuncture and you are receiving these “chakra” treatments you are being duped (although I doubt intentionally) and, to me, that is a travesty of the greatest kind.
“But the acupuncture points align perfectly with my chakras, how can you say it’s not working my chakras!?!?!?”
Which chakras? The 6+1 chakras system that we commonly refer to as “my chakras” in the west (and modern India) only became the most dominant form in the 16th century—however, there are plenty of other versions that came before and after that are still in use and practiced (e.g., 3, 15, 21, more or less depending on the practice). What about the Tibetan five chakra system? Are they somehow less efficient or capable of enlightenment because they are missing two chakras?
Secondly, the modern view of the 6+1 system tends to based on Anodea Judith’s “Wheels of Life” or books that use her book as source material., which was inspired by a crappy translation of a Sanskrit text on the chakras by a man named John Woodroffe in 1918 and Leadbeater’s “The Chakras” written in 1927. Leadbeater was a theosophist. Theosophy is closely related to the mysticism of the western mystery traditions. At this point our understanding today of the 6+1 chakras are western inspired fabrications of the original concept. To top it all off, the westernized view of chakras went back to India and influenced today’s notion of what chakras really are.
The psychological associations are purely western and modern. Jung and Freud did not hang out with the ancient Reishis back in the day (as far as I know). The same can be said for any association with bodily organs, herbs, crystals, angels, tarot, and anything else found it the western mystery traditions.
“But I’ve spent months working on my throat chakras so that I can communicate better with my significant other and it worked!”
Great! The modern system isn’t wrong, it’s just not based on classic yogic philosophy and it hasn’t had centuries to prove what works and what doesn’t. Perhaps there is a new system in the works, but if you are looking for the results found in the classic literature then you must work the ancient yogic exercises in a similar fashion.
The bottom line is, did it benefit you? If the answer is yes, then great! But I would say we should measure the word benefit in a more Vedic view. Did it lead to a more realized state of being? Or did it lead to a lessening or curing of a diseased state in the body? If the answer is no, then I would say it contributed to the illusion of reality and contributed to a further trapping in the cycle of death and rebirth.
“So then, Mr. Know-It-All, what are chakras used for?”
The short answer: They were specific to mystical practices meant to change the state of your body in order to bring about spiritual liberation.
But I digressed… Back to that original question. No, I can’t align your chakras and as an acupuncturist and trained in both the Taoist and yogic traditions, I have no clue what that even means.
“You said something about marma acupuncture; what about that? Maybe that is what my acupuncturist is doing!”
I doubt it… Marma points are similar to acupuncture points; they are related to the srotas or pathways in the body which bring nutrients and waste in and out of the body. There is some suspicion on my part and by others that early marma-puncture influenced early Chinese acupuncturists who may have taken the concept and flew with it, so to speak, creating a much more robust system, but we will never know unless some 3,000- or 4,000-year-old text magically appears showing a clear transmittal (I hope the Taoist immortals don’t strike me down for saying that).
In the book Ayurveda and Marma Therapy  it states, “We could say that the chakras are the main marmas or pranic (energy) centers of the subtle body…” Here they are not saying chakras are marmas, but that they can be viewed by their clear close relationship to marma points and by the understanding of chakras for use in therapy. They go on to say on the next page, “The important point to remember here is that through treating their respective marmas, we can treat the nadis, elements, sense and motor organs, and other factors associated with the chakras.” So, technically no, in marma-puncture, there is no needling of the chakras.
There is only one book in English on the subject and, to my knowledge, no classical text focused on the puncturing of marma points; however, it is said the tradition goes back to the Vedic times. Any modern use of marma-puncture seems to use modern acupuncture methodology to fill in the gaps. I’m not saying that is wrong, but given the amount of misunderstandings in acupuncture methodology today, I’m not convinced that this would be the best approach to use.
So I’m going to say that your acupuncturist is probably not doing marma-puncture, unless he actually says he’s doing marma-puncture, in which case I would expect them to have a serious grasp of Ayurveda to do so effectively.
MASSIVE DISCLAIMER: Firstly, I am not an academic scholar, but a practitioner of these traditions and I write based on my own knowledge and understanding. I do not write this to piss people off (although I’m sure it will), nor to seem smarter than everyone, but in order to keep the integrity of two traditions I hold dear, Chinese medicine, and Ayurveda. I am aware that many people both in the west and in the east may disagree with me because they now work with modern systems chakras (I see this in many of the modern Ayurvedic literature, and some are using it effectively), and I am okay with them disagreeing. I am also a student of the western mysteries and have used modern interpretations of chakras with some benefit, so I understand how the new view can help someone.
If these systems of medicine get broken down to a modern simplistic view of “realigning chakras” then their real benefit of helping people with disease (be it spiritual or physical) gets lost. To destroy the wisdom of the ancients because of ignorance would be terrible. Like I said above, if you are using a more modern system and it is working for you, keep doing it. If you are looking to replicate what is in the classics, do what the classics say.
May all of us reach liberation and not be trapped by the illusion of existence.