If site does and will never post GCR journals for GL Accounts associated with Bank Codes set to Use BAI it is okay to leave the Multiple deposits per batch setting off.
If the site uses Adjustments/Deposits in any manner a specific date must be chosen when Classic Bank Reconciliation will stop being used and Bank Manager will begin being used. Then for a period of time both programs will be required to be used to properly reconcile a Bank code but once everything already displaying in Classic Bank Rec has been cleared going forward only Bank Manager will be needed for reconciling.