Hi Vicki, it's correct that Advanced Payroll doesn't create individual payment lines on the journal entry and we do recommend excluding the bank transaction if the JE is already posting to the bank account. 

You can manage which accounts the journal posts to in the Payroll settings > Chart of accounts. 

Any duplicate payments already added can be removed by navigating to Transactions > Banking > Categorised > Search and select Undo beside the transaction. The transaction(s) will then move back to the For review tab where they can be excluded. 

If you have any further queries, please get back to us below. :)