This article gives some of the theoretical underpinnings of why acupuncture may help gastrointestinal issues.

Int Rev Neurobiol. 2013;111:273-94.
Effect and mechanism of acupuncture on gastrointestinal diseases.
Takahashi T.
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Abstract

Acupuncture modulates various biomechanical responses, such as prokinetic, antiemetic, and antinociceptive effects. Acupuncture treatment involves the insertion of thin needles into the skin and underlying muscle and the needles are stimulated manually or electrically. Thus, acupuncture stimulates the somatic afferent nerves of the skin and muscles. The somatic sensory information from the body is carried to the cortex area of the brain. Somatic sensory fibers also project to the various nuclei, including the brain stem, periaqueductal gray (PAG), and paraventricular nucleus (PVN) of the hypothalamus. Somatosensory pathways stimulated by acupuncture activate these nuclei. Activation of the brain stem modulates the imbalance between sympathetic activity and parasympathetic activity. Opioid released from the PAG is involved in mediating antiemetic and antinociceptive effects of acupuncture. Oxytocin release from the PVN mediates antistress and antinociceptive effects of acupuncture. Acupuncture may be effective in patients with functional gastrointestinal (GI) disorders because of its effects on GI motility and visceral pain. It is expected that acupuncture is used in the treatment of patients with functional GI disorders.
http://www.ncbi.nlm.nih.gov/pubmed/24215928