Chinese Medicine theory can be confusing to say the least and there are conflicts and competing theories for any given subject. That said, there is a fairly basic and strong set of theories upon which the medicine rests.
Zang/Fu theory and the principles of yin/yang and blood/qi can overlap to a degree which leads to some confusion initially. One common misunderstanding is to too closely associate the meridian pathology (stomach yin, for example) with the physical organ. Pathologies of the meridian do not necessarily indicate an issue with the physical organ - in fact, there is often not a problem or even an association with the functioning of the physical organ in relationship to the TCM diagnosis.
In other words, Heart Yin Deficiency, is often a way of describing a systemic problem of yin deficiency which is affecting the heart meridian (not the organ). As you get into the theory more you will look at relationships to find excess/deficiency type balances in the body. This is a way of looking at issues systematically in the sense that a yin deficiency may co-exist with a yang excess in another system. Ultimately it is these relationships that will allow you to find the "root" imbalance for a particular health problem instead of treating multiple TCM style diagnoses.
Another common source of misunderstanding is to look at the medicine too linearly or too precisely. Particularly when you are studying subjects such as the yin/yang balance. Yin and Yang are constructs of relationship, not definitive statements. So something can be yin in relation to something yang, but that same something can be yang in relation to something yin.
For understanding Blood, Qi, etc. you may find my articles on the subjects helpful (they are listed below). In these, I've tried to discuss the basic essentials of these theories.