ACH Universal handles batching in accordance with all NACHA requirements.
In addition, some banks have some additional requirements, and that is the separation of Debits from Credits in their batches.
To separate out debits and credits, simply enable the feature within ACH Setup (Settings tab > ACH Setup).
Upon starting ACH Setup, proceed to screen 5, enable the feature and complete the wizard.
--The separation of Debits and Credits is inherently contra-indicated with the use of balanced records, as a balanced batch will always create an offset debit/credit record.
--Pre-notification ($0.00) entries are not covered by this feature. Therefore, simply process pre-notes separately to create separate batches.