Hi there Louisemarie4217,
When invoices are paid via MYOB PayBy, they should automatically be marked as paid and moved out of undeposited funds. If this isn't happening, try checking if there are any pending updates for your MYOB software and ensure that your online payments service is properly configured. You can also manually match the payments to the correct invoices in your bank feeds to avoid duplication.
If the issue persists, it might be helpful to disable the automatic matching feature temporarily and manually reconcile the transactions to ensure accuracy.
Regards,
Shella