Hi brooke27
AccountRight takes the gross amount of that individual pay and then uses that against its tax tables set for the employee.
As such, if you are paying a short amount or an extra pay amount this would use the standard tax tables amount like it is a normal pay amount for that employee i.e. not look at the history. Should you need to update the PAYG amount for a pay to match what the ATO does think it should be for that particular pay/period then you can click into the Amount field for that PAYG line in the Pay Employee to update accordingly. Don't forget to put it as a negative to reduce the gross amount.