Hi Mudgee,
Thank you for reaching out and welcome to Community Forum.
If your employees are being paid electronically, the transaction would be still sitting inside the electronic clearing account. What we could do to transfer these transactions to the right bank account by making electronic payments, please make sure to do it individually if the bank feed shows it individually too.
If you prefer having it directly recorded to your bank accounts. You could edit it in Payroll > Employee > Name of Employee > Payment Details > Payment method. Also, make sure that the payment method is linked to the right account.
If you need further assistance or have any other questions let us know.
Cheers,
Genreve