Payroll - Overview and start point for users unfamiliar with payroll processes

A payroll process in summary.

  1. If necessary ensure at least one bank account is available
  2. Enter initial details of employees
  3. Define the types of remuneration (Monthly salary, Weekly pay, bonuses etc.) that will be paid via the payroll, known as Payroll Elements and at the same time the relevant account in the chart of accounts
  4. Enter PAYE and National Insurance details of employees
  5. Associate appropriate Payroll Elements to each Employee
  6. Enter any prior pay details by employee if setting up for the first time or a new employee
  7. Define any costing analysis to Branches/Funds and/or Activities
  8. Run payroll
  9. Check Pension Auto-enrolment status and initiate pension contributions if required
  10. File an (Full Payment Submission)FPS and an (Employer Payment Summary)EPS if necessary
  11. Make all payments, to employees as well as to HMRC and any pension organisations involved
  12. File all printouts and received notices

This guide covers the following:

The Personnel Menu

Users can enter and manage personnel associated with the organisation. Where appropriate contact details are maintained. Depending on the organisation type the status on any particular person can be as follows:-

Organisation and Personnel Roles
Not-for_profit Company LLP Sole Trader
Employee Employee Employee Employee
Trustee Director LLP Member
Gift-aid Claim Authorised Official Company Secretary Designated Member


When an employee role is set and the integrated payroll module is activated the Personnel Menu will display an additional sub-menu where payroll related information for each employee is managed.

Manage Employees

Each employee is presented as a data card with displaying the to which they belong, an icon to access notes and an vertical-nav-24-compact-grey action box. The action box provides for amending the employee details, tax and NI status, pension and dealing with leavers, together with information on any prior pay (Previous employment or previous payroll system), details of any employee loans or court order instructions.

To add a new employee click the red + symbol, the Add Employee screen is displayed. More information on completing this screen, depending on the legal status of the entity, is available from:

  1. Company - Employee Details/Posts Held Screen
  2. Not for Profit/Charity - Employee Details/Posts Held Screen
  3. Limited Liability Partnership - Employee Details/Posts Held Screen
  4. Sole Trader - Employee Details/Posts Held Screen

Note once they are set up the Quick Pay/Deductions facility is available to amend pay and/or deduction data for multiple employees rather than one at a time.

The Payroll Menu

The payroll menu options are divided into seven key areas.

The top two items access the usual items required to set up and run payrolls on a regular basis; Includes amending pay and deduction items and then processing single or multiple payrolls.

Payroll Batch History

All payroll batches are listed. The displayed list can be filtered by:

  1. Batch Run type - Essentially the status of a run such as , Open, Closed, Employee Reversal
  2. Payroll Admin. Group - Weekly, Monthly, Two weekly etc.
  3. Date window

Adjacent to each batch is an Action Menu. The actions available are determined by the run type and includes a DELETE option.


Provides reporting for payslips, payroll summaries as well as the Inland Revenue forms P11, P32, P45 and P60. Employee data report displays all the standing data associated with each employee. Payroll analysis report provides the details of the payroll runs for each employee during the tax year. This report may be exported in XLS and CSV format. Details of generated lists for net pay are available as well as a report identifying the accounting entries into the nominal ledger. An export file with payment extracts that can be used for BACS/online banking is available from the Payment Listing report.

Payroll - Quick Pay/Deductions

Manage Payroll

Controls payroll runs. Facilities exist to rollback a particular payroll run for an employee, close the current PAYE Year and do a bulk tax code update.

Close PAYE year closes the current PAYE year and rolls the system into a new PAYE year. Bulk Tax Code Update allows for bulk adjustment to all tax code in the payroll. This is usually used for a new tax year when HMRC issue general instructions to amend all tax codes

Configure Payroll

Provides for basic payroll and PAYE configuration data, and accesses the setup of global level details for payroll elements and pension schemes. Once set these will likely require only infrequent maintenance.

RTI - Real Time Information

From 6th April 2013 employers (with a few exceptions) report their payroll information to HM Revenue & Customs on or before EVERY PAYDAY. Each time you pay an employee you submit details about employee pay and deductions. Three submission types are used in the day to day running of payrolls and a fourth is used correct information in a prior year.

National Insurance Verification Request (NVR)

If your employee does not have a National Insurance Number or you would like to verify a number then tick the Include in Next NINO Verification Request box on HMRC CODES and TABLES tab of the Employee Payroll Detail.

Payroll - Manage Employees - Action Menu for relevant Employee - Payroll/Tax Details - HMRC Codes & Tables tab

Processing the FPS (Full Payment Summary)

Unless previously filed manually, calculated pay runs will be filed automatically on the earlier of the PAYE payment date or the cash payment date if provided. The auto-filing will occur around 11pm on the date of the payrun (not the date it was prepared if prepared earlier).

Filing the payroll run closes the payroll and the system posts the transactions to the nominal ledger accounts.

Processing an EPS (Employer Payment Summary)

An EPS is filed for a pay period when any of the following apply: -

Any figures in an EPS are on a cumulative basis for the PAYE Year and when run will include the figures for all payrolls finalised (weekly, two weekly, monthly etc.) since the last time an EPS was filed. It would be normal to run the EPS at the end of particular PAYE month.

If no payments are made in the tax month (so there is no FPS to make) you must submit an EPS and indicate no payment is due for this PAYE month. This should be done within 14 days of the end of the month. (See below) If no payments are made for a period greater than a PAYE month then this must be indicated. (See below) It is the users responsibility to determine whether an EPS needs to be filed.

Earlier Year Update (EYU), correction of errors

See separate topic. Payroll - EYU (Earlier Year Update)

Where Next?

It is suggested that for those users new to payroll and payroll processing the following route through users guides may be helpful.

  1. Payroll - Costing
  2. Payroll - Running a Payroll
  3. Payroll - Pension Schemes
  4. Payroll - Payrolling Benefits
  5. Manage Employees
  6. Payroll - Salary Sacrifice
  7. Payroll - Payroll Leavers and Reinstatement
  8. Payroll - Off-payroll Workers (IR35)