The Branch ID is used to determine the markup (%) on a shipment. Many clients have a markup associated with their company's branch.
In Magento's case we allow a client to set a markup on a current branch that they are already shipping from, or a new (virtual) branch that can be used primarily for the online / e-commerce store.
In order to set the markup needed; the Branch ID must be set. In most cases it is labeled as "HQ".