There are at least three basic theories or schools of thought related to reincarnation. At first they may seem to conflict or contradict one another, but further elucidation indicates that they all have merit. They are just different aspects of a complex mechanism. According to one theory of reincarnation, life begins with sound and color. Sound and color produce the first forms of life in the atomic structure of our being through binding the seed atoms together. At this point, life as we know it begins. It remains in a seed state or state of conception until the instinctive and intellectual cycles evolve into maturity through the process of absorption of more atoms into the astral body. This process continues until a physical body is formed around the astral body. But that is not the culmination of this theory. The cells and atoms of these bodies themselves evolve, becoming more and more refined as cycles of experience pass until complete maturity is reached in a physical body which is refined enough to attain nirvikalpa samadhi and begin the next process of building a golden body of light. According to this theory, the soul takes on progressively more advanced bodies, evolving through the mineral, vegetable and animal kingdoms, slowly acquiring knowledge through experience. There may even be a life that seems to regress, such as a man incarnating as a cow to gain needed lessons of existence. A second concept in this theory explains the lower evolutionary stage of animals, insects, plants and minerals. According to this principle, animals and lower forms of life function under what is called a "group soul." They do not have an individual astral identity, but share a group astral atomic structure. That is one reason for the lack of so-called individuality among these groups and why animals move about in herds and birds live together in flocks -- indicating the movement of the one group soul, so the theory goes. In another theory, when man dies, he goes on to the astral plane after breaking the silver cord which binds him to the physical body. During out-of-the-body experiences, this silver cord is often seen as a cord of light connecting the physical, astral and spiritual bodies. When awareness leaves the physical body, it passes through one of the chakras. If our life has been one of baser emotion and reason, we would exit through one of the chakras near the base of the spine, either the muladhara or svadhishthana, and begin a conscious existence on a lower astralplane. From there we would work out various experiences or reactionary conditions caused by congested mental and emotional forces which impressed our subconscious mind during the course of our lifetime. On the astral plane, we relive many experiences by reactivating them, creating for ourselves heavens or hells. When the lessons of that life had been learned and the reactions resolved, we would be drawn back into a family, into a new physical body, in order to gain more experience in the light of the new knowledge acquired while on the astral plane. If we have evolved to the point that our life was one of service, understanding and love, then we would exit through the next higher chakras, for that is where awareness has been polarized, and our astral existence would be of a deeper, more refined nature. However, if we had discovered and practiced a dedicated spiritual life, then our exit would be through the top two chakras, which do not lead awareness onto the astral plane but take it into the Third World of divine existence, never to reincarnate again into the physical world. After nirvikalpa samadhi is attained and perfected so that the mahayogi can go into it at will, he leaves the body consciously through the door of Brahman, the center of the sahasrara chakra above the pituitary gland at the top of the head. This depends on whether or not the golden actinic causal body, which has been developed after Self Realization, is mature enough to travel in actinic force fields on its own source :http://www.yogausa.com/mws_ch-50.php
You've partially clarified something I have wondered about. One naturally wonders, if the soul chooses where to be reborn, why would any choose what is apparently going to be an unhappy life? Obviously individuals are born into situations where they are subject to abuses, or live in dire poverty, or have dreadful diseases, etc.. This explanation (above, from yogausa.com) suggests that the soul seeks what it really needs to progress on its path, either by having wisdom that it lacks on the material plane (as its atman nature is unrestrained between lives), or by influence of the preceding life, in either case with a motivation to go forward, and without being deterred by the sort of interests that seem more pressing to us in our lifetimes. This accounts for the otherwise unintuitive choices, though it is hard to tell how one would be sure about the explanation. I saw a summary of what the scriptures say on the subject, will try to find that link again
