JDEdwards 9.0 - I am having problems setting up the automatic bank reconciliation BAI format. Has a

I have been successful in reconciling payments, but I have problems with setting up ACHs and receipts.  The  R09616 marks ACHs are reconciled with a code of "B" but it doesn't mark them as reconciled in the GL which is fine because we will reconcile them manually.  I know that unless the GL and the bank file have the same document number receipts will not reconcile automatically, I would like the receipts to be marked as cleared by the bank in the R09616 report.  This would help us with the manual reconciliation of the receipts.