Pay Run Processing

Marlin HR enables flexible and accurate pay run processing.

The Pay Run module processes employee pay for each cycle, covering standard hours, overtime, leave, one-off deductions, allowances, and tax.

Pay run details can be reviewed and adjusted for each employee before finalising, with an interim analysis report available to check figures beforehand.

Once finalised, a banking file is produced for payment, and Single Touch Payroll and superannuation reporting are handled automatically, if enabled.

Pay runs can be initialised by selecting Payrun > Payrun Processing.

Pay Run Preparation

All relevant changes and information need to be entered before initialising a pay run.

Before initialising a pay run, make sure to check:

• Employee Details
• Leave Entries

Employee Details

Main > Employee Maintenance

Make any necessary changes in Employee Maintenance:

• Add new employees
• Apply changes to employee pay rates for the period
• Apply changes to employee deductions and allowances for the period
  • Ongoing changes to deductions or allowances should be made in Employee Maintenance
  • Temporary changes that only apply to one or two pay periods can be made on individual pay runs themselves

Leave Entries

Main > Leave Entries

Add leave entries for all absences during the period (e.g. annual leave, personal/carer's leave or long service leave).

Initialising Pay Runs

Payrun > Initialise Pay Run

The Pay Run Processing module will open on the Initialise Pay Run screen.

In the Payrun Details section (top left), complete these fields:

• Pay Cycle: Select the cycle for this pay run (e.g. Weekly)
• Type of Payrun: Leave as Normal
  • For adjustment pay runs, see Adjustment Pay Runs
• Pay to Date: Enter the last day of the period you are paying
  • Every employee in the list should show a Pay Qty of 1

In the Payment Details section (top right), complete these fields:

• Date Paid: Enter the date wages leave your bank account
  • This date appears in the banking file as the scheduled payment date
• Super Paid By: Enter the date the super payment leaves your bank account

In the Employees to Pay section below:

• Select the employees being paid this pay run by ticking the checkboxes on the left
  • Casuals who did not work during the period can be left off
  • Use the All, None and Invert buttons at the bottom to quickly select or deselect employees
• Confirm there is a red Yes in the Leave Pending column for anyone who took leave during the period

Once all the required information has been entered and relevant employees have been selected, click the Initialise button at the bottom-right.

Adding Employees to Pay Runs

If you forgot to include an employee before initialising, or their missing details are now available:

• Add them to the active pay run by clicking on the add employee button at the top of the Pay Run window

This saves you delaying everyone's pay, or voiding and restarting the pay run and re-entering everyone's overtime.

Removing Employees from Pay Runs

If you included an employee by mistake, or are missing information for them,

• Remove them from the active pay run by clicking on the remove employee button at the top of the Pay Run window

This saves you delaying everyone's pay, or voiding and restarting the pay run and re-entering all the details.

Pausing Pay Runs

To pause a pay run:

• Click on the close icon at the top-right of the Pay Run module
• When you re-open the Pay Run module, the initialised pay run will still be there

Pay Run Details

Once initialised, the Pay Run screen will open.

Double-click on each employee to view and edit their pay run details.

In the Pay Advice window that opens:

• Check each employee's standard hours and overtime hours
• Check all leave entries appear correctly with the correct number of hours
• Add any compassionate leave or public holidays to be paid
• Add any one-off deductions and allowances (click Before Tax Allowance, After Tax Allowance, Before Tax Deduction or After Tax Deduction in the This Pay column as appropriate)
• Adjust tax if necessary (click Tax in the This Pay column, then Tax Adjustment)

To add any missing hours or payments:

• Click on the relevant field in the This Pay column
• Then click on the Add or Edit button below

Once all required pay run details have been added for an employee:

• Click on the Save button at the top to return to the Pay Run screen
• Repeat the process for all employees on the pay run

See the relevant Help Guides for further information about specific pay run details.

Removing Pay Run Details

To remove hours or payments:

• Click on the relevant field in the This Pay column
• Select the hours or payments to remove in the section on the right
• Then click on the Remove button below

Refreshing Employee Details

Where possible, make changes to employee details and leave entries before initialising.

If you make changes afterwards:

• Double-click the relevant employee on the pay run, to view their details
• Click the Reset To Standard Pay Advice icon
• Respond Yes to the confirmation prompt

Interim Reports

Employees Not Appearing

An employee may not appear on a pay run for one of these reasons:

Status is Terminated:

• Check their Status field in Employee Maintenance
• If it is "Terminated", you will need to set them up as a new employee

Status is Inactive:

• Check their Status field in Employee Maintenance
• Set it back to Active, if required

New employee has incorrect dates:

• Set their Joined Date in Employee Maintenance to the employee's first day of work
• Set their Paid To field to the Pay to Date of the last Normal pay run before they started

You can the add them to the pay run.

Leave Not Appearing

A leave entry may not appear on a pay run for one of these reasons:

Pay to Date is wrong:

• Check the From Date and To Date at the top of the initialised pay run
• If either is incorrect, void the pay run, select the correct Pay to Date and initialise again

Leave entry was saved after the pay run was initialised:

• Void the pay run
• Initialise it again
• Select the employee
• Click the Reset To Standard Pay Advice icon at the top

Leave falls outside the pay period:

• Open the leave entry
• Check that some or all of the From and To dates fall within the pay period

screenshot

Employee Maintenance settings are incomplete:

• Open their Pay Details tab in Employee Maintenance and check that:
  • At least one day is ticked in Ordinary Days of Work
  • Ordinary Hours Per Pay (below) is not zero
  • Standard Hours in the Earnings box (top right) is not zero

Finalising Pay Runs

Once you have checked all pay run details and figures for each employee:

• Click on the Finalise button at the top-right of the Pay Run screen

If Single Touch Payroll is enabled, a pop-up will open.

In the Single Touch Payroll declaration pop-up that opens:

• Tick the Declaration checkbox at the bottom
• Click Proceed

In the Email Banking File pop-up that opens:

• Click Yes to email the banking file to the specified address

where is this set up?

A pop-up will open summarising the pay run finalisation:

• Click Ok to run the backup program.

Pay Advices and Reporting

See the Pay Advices and Pay Run Reporting help guides for information on how to access and print pay advices and other relevant reports.

SuperStream Files

See the SuperStream help guide for further information about how to produce and upload SuperStream files.

Missed Employees

If you accidentally leave an employee off a pay run you can re-enter the same pay-to date period to pay them:

• Employees who have already been paid will have a red "0" in their Pay Qty column and cannot be selected
• Unpaid employees will have a "1" and can be selected for payment

Skipping Pay Periods

You cannot skip a pay period. Periods must be paid in the correct sequence.

If you want to pay an employee in advance, you should run each pay run for them in the correct date order.

advance payments

This ensures that there is a separate pay advice, bank file, pay journal and STP submission to the ATO for each period.

advance payments

Skipping Employees

Casual employees should only be included on pay runs for periods in which they worked (their Pay Qty will always be "1").

However, you cannot leave full time or part time employees off pay runs, even if you are not paying them for that pay period:

• Leaving them off would mean their Paid To date would not be updated and their Pay Qty (payable pay periods) would increase
• HR would then calculate their tax as if it were earned over multiple periods, which would be significantly lower than it should be, perhaps even zero (even if you reduce their default hours, allowances, deductions)
• The employee would also receive leave accruals for every period

Unpaid Periods

Include employees on unpaid periods on each pay run:

• Enter any hours worked as Standard Hours (normal hours minus absent hours)
• Add the absent hours as Unpaid Leave

If the employee is absent for the whole period:

• Enter their normal work hours as Unpaid Leave
• Leave Standard Hours at zero

To add Unpaid Leave:

• Click Add
• Select Unpaid Leave
• Enter unpaid hours
• Click OK

For all unpaid periods:

• Zero any unpayable overtime or allowances
• Also zero any deductions, to avoid negative net pay
• You can also include a comment on the employee's pay advice with the reason and dates for the unpaid leave

Their Paid To date stays current, ensuring earnings and tax are correctly calculated over a single pay period when they return to work.

The employee will receive no payment or superannuation for the unpaid hours, and their net pay will be $0 for those hours.

If they do not accrue leave, the unpaid hours are reported to the ATO via STP.

Advance Payments

See the Advance Payments help guide for further information.