The amount in the Profit and Loss report is the gross amount, which includes what the employee has been paid plus the the PAYG tax. Until the PAYG tax is actually paid the the ATO it will be a liability to your business and will also be showing in the balance sheet.
To pay your payroll liabilities (including your PAYG tax), navigate to the drop down menu Employees, then select Payroll Taxes and Liabilities > Create Custom Liability Payments. Make sure that the date range reflects the range of liabilities that you want to pay.
Then you just select the bank account and the pay date. This will remove the liability from the balance sheet and record the transaction in your bank account. Your Profit and Loss report will remain unchanged (as it should). The gross amount of payroll should display in this report.