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Payroll

STP-2 payroll built around your team’s recorded hours.

Payroll in the Marlin product family, with pay runs, leave, banking files and reporting connected to your workshop platform.

PAY RUN 41

Time and attendance

Week ending 12 October

38.0Ordinary hours
048h
Mon
7.6 h
Tue
7.6 h
Wed
7.6 h
Thu
7.6 h
Fri
7.6 h
Recorded hoursBreak
Payslip

Senior technician

Week ending 12 October

Ordinary pay$1,520.00
PAYG withheld−$289.00
Super contribution$182.40
Net pay$1,231.00
STP Phase 2 reporting

How HR fits together

From employee records to a finished pay run

Keep the employee details, hours, leave, banking and reporting together. Follow the payroll workflow, then explore the tools behind each stage.

Or see the full feature list

01 / Employee records

Start the pay run with the right employee details

Maintain each employee’s payroll information, defaults, rates and department allocation. Earnings, deductions and entitlements are attached to the employee record, so the next pay run has the right starting point.

Set up the employee
Keep payroll information and the employee’s employment details together.
Apply checked defaults
Use employee defaults, then review the settings for that person.
Allocate the cost
Split the employee across departments when required.
Employee → rates → entitlements

02 / The pay run

Review the hours and pay before you finalise

Initialise the pay run for the right cycle, enter or review the recorded hours, and check earnings, allowances and deductions. Marlin HR produces the payroll outputs and pay journals from the run.

Use recorded hours
Work from entered hours or configured attendance connections.
Check the totals
Review employee pay details before finalising the run.
Correct with a record
Use the documented adjustment, reversal or correction process.
Hours → earnings & deductions → finalised pay

03 / Leave records

Keep leave balances beside the payroll record

Maintain leave types and entitlements, record leave entries and review their effect on balances. Leave accruals, adjustments and payouts have their own documented workflows rather than being a note outside payroll.

Maintain entitlements
Set up the leave types and accrual settings in use.
Process leave entries
Enter, review and process leave against the employee.
Check the balance
Review accruals, balances and any required adjustments.
Entitlement → leave entry → balance

04 / Payroll payments

Prepare wages and super from the pay run

Generate wage banking files and work with the superannuation records created through payroll. SuperStream files and the optional Payday Super Assist connection support the configured super processing workflow.

Prepare the banking file
Create the wage payment file for the payroll dates.
Maintain super details
Keep funds, employee contributions and payroll super settings together.
Choose the processing setup
Use the documented files or enable the Payday Super Assist integration.
Pay run → banking file → super records

05 / Payroll reporting

Report the pay run and follow its status

STP Phase 2 reporting uses the classifications and codes maintained in payroll. Check the submission process and work through the documented year-end review and finalisation steps.

Map the payroll data
Maintain the STP classifications for employees and payment types.
Check submissions
Follow the documented reporting and response process.
Close the payroll year
Review and finalise the year’s reporting in Marlin HR.
Pay run → STP submission → year-end review

06 / The payroll accounts

Follow payroll through to the ledger

Pay journals carry payroll into the configured accounting records. The GL Reconciliation Report helps identify differences, while saved reports and employee earnings reports make the pay run easier to review later.

Post the pay journals
Use the configured payroll GL and supplier accounts.
Review differences
Compare payroll records with the general ledger.
Keep the reports
Save report settings and retain reports in Report Keeper.
Payroll → pay journals → GL reconciliation

Full feature list

Explore the Marlin HR feature set

Find the payroll task you need and open the maintained guide for the detailed process.

6 features in employees & pay setup

Employees & pay setupEmployee records

Maintain employee details and payroll information in a single record.

Employees & pay setupEmployee defaults

Use defaults for new employees and review their payroll settings before the first pay run.

Employees & pay setupCasual & salaried staff

Use the documented setup for casual and salaried employees.

Employees & pay setupMultiple rates & departments

Maintain multiple employee pay rates and split payroll costs across departments.

Employees & pay setupModern Award indicators

Assign an award classification and review pay-rate indicators. HR does not enforce or overwrite the employee’s configured rate.

Employees & pay setupEmployee notes & documents

Maintain employee notes, reference documents and development tracking.

Browse all HR guides 154

Step-by-step instructions, reference material and system setup.

Ad Hoc ContributionsAdjustment Leave EntryAdjustment Pay RunsAdvance PaymentsAllowancesApril–June Submissions (2025–26)ATO Super Clearing House ClosureAudit LogsAUSkeyBack PayBackupsBanking FileBanking FilesBefore the First Pay RunBirthdays and AnniversariesBonus & Comission PaymentsCancelling Leave EntriesCashing-Out LeaveCasual EmployeesCasual TerminationsClosing a BusinessCompany Details and Payroll ContactCompassionate LeaveComplianceCustom FieldsDeceased EmployeesDeduction TypesDeleting EmployeesDepartmentsDuplicate Employees ErrorsEarnings TypesEducation Debt RepaymentEmployee DefaultsEmployee EarningsEmployee FormsEmployee FormsEmployee Fund ChangesEmployee Loan RepaymentsEmployee MaintenanceEmployee Notes and DevelopmentEmployee Payroll InformationEmployment Separation CertificateEnd of Year (EOFY)EOFY FAQEOFY Quick RefErrors and HangsFavouritesFinancial YearsFixing Missing Salary Sacrifices to SuperFringe Benefits Tax (FBT)Fund Employer Number (FEN) ErrorsGarnishing WagesGL AccountsHandy LinksHR 2.2.1 - STP-2 ActivationHR 2.2.2HR 2.3.1HR 2.3.2HR 2.3.3HR 2.3.4HR 2.3.5 EOFYLeave AccrualLeave AccruedLeave AccruedLeave Balances and AdjustmentsLeave EntitlementsLeave Entry ProcessingLeave LoadingLeave TypesLeave Without PayLong Service LeaveMedicare LevyMixed Leave LoadingModern AwardsModern AwardsMultiple ABN SubmissionsMultiple RatesMyGov AccountsNet Pay RoundingOrdinary Time Earnings (OTE)Outstanding Loan BalancesOverviewPaid Family and Domestic Violence LeaveParental LeavePasswords and Access LevelsPay AdvicePay AdvicePay CyclesPay Date & Scheduling PaymentsPayday Assist OverviewPayday Assist Set UpPayday Super webinar for Marlin HRPAYG Witholding ReportsPayment SummariesPayment SummariesPay Qty & Pay To DatesPay Run CorrectionsPay Run Dates and GL PeriodsPay Run Initialisation ScreenPay RunsPay Run TipsPenalty & Overtime RatesPre-1993 Leave AccrualsPrevious YearsProgram UpdatesPublic HolidaysReactivating EmployeesReconciling GL to HRRelease NotesReportable SuperannuationReport KeeperReportsReversing Pay RunsRostered Days OffSalaried EmployeesSalary SacrificeSaving ReportsSavings AccountSingle Touch Payroll Phase 2 (STP-2)Single Touch Payroll Reporting (STP)Stapled Superannuation FundsStartup and LayoutSTP-2 Reporting CodesSTP-2 Reporting CodesSuperannuation FAQSuperannuation Guarantee Rate (SGR)Superannuation Set UpSuperannuation Top-UpsSuperChoice Log InSuperChoice PaymentsSuperChoice RegistrationSuperChoice SubmissionsSuperChoice Validation IssuesSuper ContributionsSuper FundsSuperStreamSuperStream FilesSupplier AccountsSystem Information and DefaultsTax AdjustmentsTax File NumbersTax on ad hoc PaymentsTax ResidencyTax ScalesTerminated EmployeesTerminated EmployeesTermination Pay CorrectionsTermination PeriodsTime In LieuTransferring EmployeesTwo-Week CyclesUnprocessed Leave EntriesVideo TutorialsWorkers' Compensation

Have questions about a feature or your setup? Talk it through with our team.

Talk to HR sales
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