Alignment is a concept that refers to the state of the physical reality as a reflection of Consciousness. When physical reality accurately reflects the will, intent, and desires of Consciousness we say that physical creation is in alignment with Consciousness. When the physical universe is "off" in some way, we say that physical creation is out of alignment or (in severe cases) disjunctive of source Consciousness.
Reality is "in alignment" with Consciousness when it is a pure and uncorrupted expression of Consciousness (with a capital "C").
Alignment may refer to the general state of physical reality as a reflection of Consciousness, or it may refer to specific instances/examples of alignment, as for example the alignment of Bodily Ego with Spiritual Ego. In this case, alignment refers to the extent to which the Physical Unit is acting as an “appropriate and responsive” physical unit for Resident Monadic Consciousness. The easiest way to think about this is to think about a car. If you get into a car and you hit the gas, but the car slows down, or if you turn the wheel left, but the car turns right, the car is out of alignment (i.e. unresponsive) to the intent of the driver. It is the same with your physical body. If the RMC that "owns" the Physical Unit wants the Physical Unit to do one thing, but it does another, the body is out of alignment with RMC.
To the extent that the physical unit is functioning as an appropriate and responsive vehicle for the resident monadic consciousness (RMC) we may say that the physical unit is in alignment with its RMC. A physical unit that is in alignment with its own RMC perceives, thinks and acts in accordance with the perceptions, thoughts, and desires of its own RMC (Sosteric, SA1). A physical unit which, because of (for example) Toxic Socialization and Indoctrination, thinks and acts in ways that are against the nature and/or wishes of its RMC, or a physical unit that is unresponsive to the wishes of its RMC, may be said to be out of alignment.
Alignment is a requirement of the Awakening, Activation, and Ascension of the physical unit. A physical unit that is out of alignment may have difficulty with the process of awakening and activation. Acts that the physical unit engages in may be painful to the RMC and therefore the RMC may be forced to remain "at a distance" from the physical unit (thereby lowering the CQ of the physical unit. At the same time, the uncompromising nature of the RMC may cause disjuncture and discomfort in the physical unit and as a result the physical unit may itself push away (i.e., repress) the RMC.
Alignment of the physical unit is a key developmental task. When not attained in childhood, alignment can be attained in adulthood by encouraging the physical unit to engage in right thinking and right action and by providing right environment.
Alignment of the physical unit with Consciousness/God is a common theme in traditional spirituality. The Jewish Torah contains extensive and detailed "laws" (i.e. statements of alignment) that God gave Moses indicating how the people were to behave in relation to God/Consciousness, and with each other as well (Ehrman, 2007).
In the Christian bible, Paul speaks of "righteousness, self control," (Acts, 27: 17) both of which are components of alignment, righteousness being a state of strong moral/behavioural alignment with Consciousness, and self control (i.e. control of the physical vehicle) a basic requirement of incarnated Consciousness.
Alignment has also been a concern, from time to time, among psychologists. In an 1960 radio interview, Abraham Maslow suggest that there were "basic, underlying, human standards that are cross-cultural" (Maslow, 1961). These standards, which according to Maslow were universal, should be used to govern the social order.
Alignment is a significant concern of knowledgeable kundalini practitioners. As GM CKS notes, "When the Kundalini is awakened, the positive and negative qualities of the person will be magnified to a very high degree. Kundalini energy is like fertilizer. Whatever seeds are in the ground will be stimulated to grow. So whatever ancient seeds a person possesses, whether good or bad, will be magnified. This is why a person going into the spiritual path experiences intense inner battles. Therefore, it is important to practice inner purification." (Sui, 2016).
Sharp, Michael (B0). Lightning Path Book Zero: Introduction to the Authentic Spirituality. Lightning Path Press.  Sharp, Michael (BOOK3). Lightning Path Book Three: The Basics. Lightning Path Press. http://press.thelightningpath.com/product/lightning-path-book-three-basics/
Sharp, Michael (GA). The Great Awakening: Concepts and Techniques for Successful Spiritual Practice. http://press.thelightningpath.com/product/great-awakening/
Ehrman, Bart D. 2007. Misquoting Jesus: The Story Behind Who Changed the Bible and Why: Harper One.
Maslow, Abraham H. 1961. "Eupsychia—The Good Society." Journal of Humanistic Psychology 1 (2):1.
Sui, Choa Kok. 2016. How to Safely Awaken the Kundalini! http://www.awarenessmag.com/julaug1/JA1_SAFELY_AWAKEN.HTML
Sosteric, M. (SA1). The Science of Ascension: A Neurologically Grounded, Spiritually Sophisticated Theory of Mystical/Spiritual Experience. Unpublished.