There are two approaches used for processing of bank account transfers worldwide. These approaches are one-phase processing and two-phase processing. In both approaches the funds are cleared by a nation-wide financial authority called a clearing house. The difference between the two systems is as follows. In a two-phase system a merchant cannot start actually processing transactions until he submits the list of bank accounts through which he is going to process. Only after these accounts are registered by the financial authority and the merchant gets respective mandates, he can start processing transactions through these accounts. One-phase processing system is less complex, but the two-phase system is more reliable.
More information on bank account transfer systems can be found in the respective article on Paylosophy.