That's a good question Lucia!
The brain processes information and from there nerves (and hormones) bring it into the organs. Some information is directly processed in the Autonomic Nervous System, but as we know the vagus nerve (part of the ANS) has nuclei in the brain stem, so to me the brain stem and ANS merge. 
The term "relay" was used by Dr Hamer to describe certain points and regions in the different brain layers that show a "fingerprint" when a certain organ tissue reacts upon a conflict. 
To my knowledge there is often no direct neuronal connection from, for example, the cerebellum to the dermis for reinforcement of the tissue. Yet  the dermis is impacted by conflicts of perceived attack, at the same time as a "fingerprint" can be observed in the cerebellum. Scientifically, more research would be needed to explain this and to find the mechanism at play. 
For us as practitioners however, it's enough to be aware of the biological function of the organs with which they try to help us process and resolve our conflicts, and the "old brain" and "new brain" types of conflicts and the "plus or minus" reaction patterns.

Scientists usually describe processing information as a function of the brain. Especially conscious functions are attributed to the thalamus and the cerebral cortex. So, as Craig mentioned in our last session, talking about the functions of the brain can get confusing when we take related organs into play... it's like two specialist languages, we need to make clear which one we use in a conversation.