Normal method In most cases, allowances and deductions are set up in the employee record, and don't change from pay period to pay period. However, sometimes you may need to adjust or add an allowance or deduction for just one pay. In these cases, the best way is to adjust the allowances or deductions when you are preparing the pay.
1 Choose Prepare Pays from the Activities menu, or click Pays on the toolbar to display the Pays Summary window.
2 To enter or modify the employees pay, click to select the employee. Click Activities>Edit Pays. The Employee Pay Method box, at the top left side of the window shows the pay method for the employee. Edit pay details on the pay window. For further information on entering hours and making modifications, refer to one of the following:
If the employee is paid using the Spreadsheet method, the Spreadsheet Entry window is displayed. Click the drop-down 
list arrow in the Details column to display the Pay Details window.
Note You cannot edit a past pay unless the ž Edit Past Pays checkbox has been selected. You also cannot edit a past pay if you have been set up as a user without the rights to edit a past pay.
3 If the pay covers more than one pay period, enter the number of pay periods in the Pay Periods box.
For example, if an employee is going on annual leave for three weeks, and is being paid the entire three weeks in advance in addition to the current pay, so "4" weeks is entered. The employee will then be automatically excluded from the next three pay runs, and tax will be calculated accordingly.
Note When you make any payment that covers more than one pay period, don’t forget to also adjust any allowances or deductions accordingly.
4 Click on the Deduction tab, and enter or edit any deductions that will be taken from the employee's pay for this pay run. DO NOT use deductions to record salary sacrifice, this is done through the superannuation section.
Deduction – Select the deduction to be taken from the employee's pay. If the deduction you want hasn't yet been set up, type in the name and then press TAB. Click Setup on the Quick-Add pop-up window to add the deduction to the Deductions List. When you select an existing deduction, Elite Payroll will automatically enter the defaults for the deduction.
ID – Enter the ID for this employee's deduction. By entering an ID it becomes easier to identify the deduction for a particular employee on a report.
Amount – Enter the amount of the deduction.
Ex Tax – If the deduction is tax-deductible for the employee—to be deducted from gross wages before tax is calculated, select Yes in the Ex Tax column. If it isn't tax-deductible—to be removed from the net after tax is calculated, select No. Note that most deductions are not tax deductible.
To add a new line, click Insert, or Tab to a new line. Enter details as per the above. To delete a line, select the line and then click Delete. Click OK to confirm that you actually want to delete the line.
5 Click on the Allowance tab, and enter or edit any allowances that are to be paid to the employee this pay run.
Allowance – Select allowance to be added to the employee's pay. If the allowance you want hasn't yet been set up, type in the name and then press TAB. Click Setup on the Quick-Add pop-up window to add the allowance to the Allowances List. When you select an existing allowance, Elite Payroll will automatically enter the defaults for the allowance.
% or Units – If the allowance is a percentage of a pay rate, enter the percentage amount. If the allowance is per pay period, enter the number of pay periods that are being paid. If the allowance is for an item, such as kilometres, enter the number of kilometres.
Based On – Select what the allowance is based on.
Allowance based on hours worked – Enter 0 in the % or Units column and select a pay rate from the Based On column, the allowance will be calculated as the number of hours worked for that pay rate times the amount entered in the Amount column. This will be calculated when you process the pay. For details, see How do I pay an allowance based on the number of hours worked?
Amount – Enter the amount of the allowance. If the allowance is per pay period, just enter the amount for one pay period—Elite Payroll will calculate the total allowance amount to pay.
Super – Select Yes if you want the allowance to be included in superannuation calculations. Select No if you want the allowance to be excluded from superannuation calculations.
Ex Tax – If the allowance is non-taxable—to be added to the net after tax is calculated, select Yes in the Ex-Tax column. If it is taxable—to be added to the gross before tax has been calculated, select No. Whether an allowance is tax-exempt or not depends on a number of factors, including the type of allowance, the amount, and the income of the payee. For full details, see Taxation of allowances.
Customer:Job – The allowance can be assigned to a customer and job.
Class – The allowance rate can be assigned to a specific class. Enter the class, or select the class from the drop-down list.
To add a new line, click Insert, or Tab to a new line. Enter details as per the above. To delete a line, select the line and then click Delete. Click OK to confirm that you actually want to delete the line.
Note Allowance details such as if the allowance is Payroll Tax or WorkCover exempt, where the allowance appears on Payment Summaries, and calculation thresholds, are set up through the Allowances list.
6 Manual tax – If for some reason you need to manually adjust the tax, Elite Payroll will place a check mark in the ž Manual Tax checkbox at the bottom of the window. You should only do this if you have a very good reason. If the ATO audits you and you cannot explain why the tax is different to what it should be, you may be fined. To revert to the calculated amount, click to remove the check mark from the Manual Tax checkbox.
7 Enter or modify other pay details, if required, and click OK.
8 Process the Pays with the other employee pays.
See also
Process a pay with allowances and deductions – Normal Pay method
Process a pay with allowances and deductions – Spreadsheet method
Process a pay with allowances and deductions – Timesheet Pay method