illustration from Barbara Brennan, Hands of Light, Bantam Books 1987, p.44

The secondary chakras are the chakras described by Theosophy, the New Age movement, Christopher Hills, Barbara Brennan, and many others.   Unlike the archetypal Primary chakras they have a specific form (usually described as vortexes of energy), colour and a specific precise location in the auric bodies (although these qualities will vary according to the individual).  These chakras are etheric and pertain to the Eso Being, which includes not only the ordinary everyday consciousness but even psychic, occult and many transpersonal and mystic states.

The chakras located at the front (feeling) and rear (will) of the body, as described by Barbara Brennan, .  The psychological characteristics of each chakra are emphasised, but there is no conception of a circulation of energy. The idea of an energy axis down the midline of the body, rather than along the spine, is not found in other books and may be a result of artistic (mis)interpretation. diagram from Hands of Light, Bantam New Age books, 1988, p.46.

The microcosmic orbit showing the yin (descending, in black), and yang (ascending, flame) points which can be equated with the Secondary chakras.  This is a dynamic conception involving the circulation of Ch'i energy.  However there is little emphasis on the psychological aspects of these centers. diagram from  Mantak and Maneewan Chia Awaken Healing Light of the Tao (Healing Tao Books, 1993), p.170.

The secondary chakras can be awakened into a rhythmic microcosmic orbit through meditation and disciplined practice (this is the initial stage of Taoist Nei Tan or Internal Alchemy).   This microcosmic orbit - called the Circulation of the Light - is actually (I believe) the equivalent of the macrocosmic cycle of evolutionary metamorphosis, as described in theosophical and anthroposphical teachings (Rounds, Root Races, etc).

In occult, spiritual, and New Age literature the secondary chakras are almost always confused with the Primary Major Chakras.  This confusion is due to the imperfect state of esoteric knowledge at the moment (equivalent to science in the 16th or 17th century). In fact the two types of chakra are quite distinct and easily distinguished.  The following table gives some contrasts: