Hi
The correct thing is happening when you match the transaction in your bank to the electronic payment.
The payments to the suppliers and your employees have been , as you say, already been entered by way of the electronic clearing account pay bills pay employees transaction in myob.
Your accountant will be able to drill down into the electronic payment to find the payments allocated to it, but each payment can also be seen against each individual invoice.
Is there another issue that is causing concern to your accountant , as this process is common amongst most financial systems?
Hope that helps to clarify
Lisa