Chakras and Dan-tiens are energetic structures from two different schools: the Hindu Yoga and Daoist Alchemy. There may be similarities, but also differences. To visualize for example, Chakras are traditionally depicted as spinning wheels (in non-Tantric schools where they are more active in function) and Lotuses (in Tantric schools where they are more passive conduits that act as pathways to the sentient, cosmically intelligent Shakti or Goddess who appears in macrocosm as Kundalini).
Dan-tiens are a lot more ‘physical’ while Chakras are more ‘energetic’. If one had to combine the two schools, Dan-tien would be like a storage container of Chi in which spinning wheels of energy aka Chakras are swimming. The three Dan-tiens are like cauldrons in which energy is stored and refined and circulated, affecting physical organs around them - in that, they have similarities to Chakras. They are the cauldrons which transmute respectively, Jing -> Chi, Chi -> Shen and finally, Shen -> Wu-ji, unbridled, non-corrupt pure energy or Dao. While all three of them deal with physical organs around them, they can be mapped to physical, emotional and spiritual aspects respectively, in terms of their primary function.
In alchemical practices such as Taiji, Qigong, Maoshan sorcery etc., these Dantiens are systematically used, usually starting with the lower one, to cultivate and refine energy. Water paths work on energy descending from the upper to the lower one, while the more common fire paths deal with energy flow upward, starting with cultivating the lower Dantien first.
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