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In treating diseases, one must understand the concepts of Root (Ben) and Branch (Biao). The initial pathogenic factor contracted is the Root; the disease manifestations that transmit subsequently are the Branch. For instance, if a mild disease is contracted first and later gives rise to a severe disease, the mild disease should be treated first, followed by the severe disease, so that the pathogenic qi may subside. This is because treating the Root achieves this result. If the Root is treated first, although there may be more than ten symptoms, they will all disappear. However, if the Root is not treated first, but instead the Branch is treated, the pathogenic qi will become more intense, the condition will worsen, and it will become incurable. In cases of fullness in the middle jiao (abdominal distension), regardless of Root or Branch, the fullness in the middle jiao should be treated first, as it is an urgent condition. If abdominal distension is accompanied by constipation (obstruction of bowel movements and urination), regardless of Root or Branch, the constipation should be treated first, followed by the abdominal distension, as this is even more urgent. Apart from constipation and abdominal distension, the Root should always be treated first; this must not be neglected.

Suppose the Liver receives pathogenic heat-fire from the Heart. This transmission comes from "before" (in the sequence of generation, Wood generates Fire, so Heart is the Child of Liver), constituting an Excess Pathogen (Shi Xie). One should drain the Child organ's fire (Heart fire). Thus, the Classic states: "Root then Branch," treat the Root first. Use herbs entering the Liver Meridian as guiding agents, and use herbs draining Heart fire as the Sovereign (Jun) herb. This is the method for treating Excess Pathogens.

Suppose the Liver receives pathogenic factors from the Kidney. This transmission comes from "after" (Water generates Wood, so Kidney is the Mother of Liver), constituting a Deficient Pathogen (Xu Xie). One should tonify the Mother organ's water (Kidney water). Thus, the Classic states: "Branch then Root," treat the Branch first. Use herbs entering the Kidney Meridian as guiding agents, and use herbs tonifying the Liver as the Sovereign (Jun) herb. This is the method for treating Deficient Pathogens.

When using the flavors of herbs, one must consider whether their flavors are appropriate. When using the Qi (thermal nature: cold, hot, warm, cool) of herbs, one must ensure it suits the condition. By recognizing the Root and Branch of the disease, as well as the Cold-Heat, Deficiency-Excess, severity, and urgency of the Zang-Fu organs, one selects the Qi and Flavor of the herbs and formulates prescriptions according to the symptoms. The herb that primarily treats the disease is the Sovereign (Jun); those assisting the Sovereign are the Ministers (Chen); those responding to the Ministers are the Envoys (Shi). This follows the appropriateness of the disease to assist in composing the prescription. A formula with one Sovereign and two Ministers is a "Odd" (Qi) system. A formula with two Sovereigns and four Ministers is an "Even" (Ou) system. Diseases near the throat are considered "near"; near conditions use Odd formulas. Diseases in the Liver and Kidneys are considered "far"; far conditions use Even formulas. Diaphoretic methods (sweating) should not use Odd formulas; purgative methods should not use Even formulas. Tonifying the Upper Jiao or treating Lower Jiao diseases requires a slow/gradual formulation; slow formulations have light/thin Qi and Flavor. Tonifying the Lower Jiao or treating Upper Jiao diseases require a rapid/intense formulation; intense formulations have heavy/thick Qi and Flavor. Light/thin herbs should be taken frequently in small doses; heavy/thick herbs should be taken in large doses at once.