The Employer menu is where you can set up all your employer details, most importantly, you can allow submissions to HMRC by filling in your PAYE reference and Accounts office reference.

Employer > Employer Details 

The place to start in Payroll is the Employer > Details menu.

The Employer name will have been defined by the organisation name used during registration.

The HMRC office name, PAYE reference and Accounts office reference can be found in your HMRC’s Online Services portal or on paperwork received from HMRC. It is important to fill in the PAYE reference and Accounts office reference, as this will allow you to submit RTI to HMRC via Payroll.

Below is a tickbox for those who can claim employment allowance, that is, up to £3000 a year off your NI bill. In order to be eligible, you must be a business or charity paying Employers’ Class 1 NI.

You can enter a payment method and add below this a BACs payment sort code.

Next, you will see a Payroll HMRC contact dropdown. If you use our Accounting module, it is important to select the relevant HMRC contact so that when importing payroll into accounts, the bills will be allocated to the correct supplier.

Likewise, you will have to select the relevant Pension Entity set up in Accounting in the drop-down provided so that when importing payroll into accounts, the bills will be allocated to the correct supplier.

Employer > Address

Click on the Address link on the left hand side, to be able to fill in the company’s address.

Employer > Pension (Employer Pension settings)

Finally, click on the Pension tab. The staging date is the date your automatic enrolment duties come into effect.

An employer can choose to delay assessing and therefore enrolling. Enter the postponement date if you plan to assess at a later date.

Enter a re-enrolment date. Re-enrolment is the process where your client must re-enrol certain staff into a pension scheme that can be used for automatic enrolment, if they’re not already active members of one.

Make sure to hit the Save button after any changes.


The settings menu allows you to show and hide unused payroll periods and has several Payslip options.

Settings > General

In the general settings you can select the payroll frequencies that you would like to be able to see under the Payroll > Overview menu. If you only pay your employees a monthly salary then you can disable all other frequencies for clarity. 

You can also enter the specific pay day for each frequency appropriate to you. The 1st day in the Weekly, Fortnightly, Fourweekly and Quarterly is the first day of the new tax year i.e. whichever day the 6th April aligns with.

The Payslip can be emailed directly to your employee by ticking the Enable payslip emails by default checkbox. You can also specify the day on which the Payslip should be emailed using the drop down box below this. Finally, you can update the colour of the payslip using the colour matching tool.

Settings > Advanced

The advanced settings allow you to re-map the account codes used on the bills that are created when payroll is imported into the Accounts module. 

How to change Payroll Account codes

You can create new accounts in the Accounts module and map them to the appropriate Payroll code.

How to add new account codes

Settings > Email Templates

On the Email templates menu, you can update the look and default message on payslip emails.

How to customise the Payslip email sent to your employees


The Employees menu allows you to set up new employees/directors or edit/remove existing ones.

Employees > View

From the view menu you can switch to view all, current or former employees. You can also view a P11 or P45 (for former employees). As long as you have not processed any pay for an employee, you can remove them if you have created a duplicate.

Employees > View - Add Employee/Director

From the View menu click on the Add employee/director button to begin filling in the details of a new employee/director.

Employees > View - Import supplier

You can import suppliers from the Accounts module using the Import supplier button on the View menu. You can select the supplier from the drop down list and then hit the Import button.

Employees > Statutory Payments

To calculate SMP, the employee's average weekly earnings must be greater than £111, Also the employee must have worked for you for 26 weeks going into the qualifying week (i.e. you must have processed pay in Payroll for this employee for the previous 26 weeks). Select the employee and enter the baby due date to begin.

How to calculate Statutory Maternity Pay (SMP)

Employees > P60

P60s are available to print and email as soon as the current tax year has ended on the 6th April. 


Payroll > Overview 

Depending on the Payroll frequencies you have enabled on the settings menu, the system will display Monthly, Weekly, Fortnightly, 4-Weekly, Quarterly and Annual in the drop down list. Each frequency overview will show a table with the total gross, taxable deductions, PAYE (employer & employees), NICs (employer & employees), student loan, pension (employer,employees & combined), other income, other deductions, net pay, employment allowance, HMRC bill and wage bill. You can switch between tax years to view the history of Payroll.

Payroll > Periods

Again, depending on the Payroll frequencies  you have enabled on the settings menu, the system will display Monthly, Weekly, Fortnightly, 4-Weekly, Quarterly and Annual in the drop down list. Clicking on a period will take you to the current period within the appropriate frequency.

Payroll > RTI

Real Time Information requires employers to report payroll information about tax and other deductions under the PAYE system in real time. Employers using RTI are no longer required to provide information to HMRC using via a P35 and P14 after the end of the tax year, or to send Forms P45 or P46 to HMRC when employees start or leave a job. 

Payroll > RTI > Submissions

The submissions menu is an audit of the RTI you have sent to HMRC. This menu will list all the EPS and FPS submissions, the tax year they relate to, the correlation ID of the submission (this is a receipt sent from the HMRC system to confirm that they have received it), the submitter, the time and the status.

Payroll > RTI > File EPS

An Employer Payment Summary allows you to reclaim statutory maternity, paternity, adoption or shared parental payments, Employment Allowance,  Construction Industry Scheme (CIS) deductions as a limited company. You must also report any periods of inactivity. 

Payroll > RTI > File FPS

An Full payment submission is created each time you process payroll for an employee/director. You must send the FPS  to HMRC on or before your employees’ payday, even if you pay HMRC quarterly instead of monthly.

Payroll > HMRC bill report

The HMRC bill report is the break down of what needs to be paid to HMRC each period. 


All employers in the UK are legally required to enrol employees into a qualifying pension scheme and make contributions.

Pensions > Pension Scheme

Once you have set up a pension scheme with a provider, you will needs to add some details for this into Clear Books Payroll. If you already have an existing pension scheme, you will also need to add this into Clear Books Payroll. Fill in the details of your pension scheme on this menu - once this is added you can assign this to employees as described in the Employee heading above.

Pensions > Reports

Assess the Workforce

Clear Books Payroll has a report that will assess your staff, enabling you to see who is and who isn't eligible. Please note, we assess using tax pay reference periods (starting 6th April) rather than regular wage periods (1st-31st).

Employee Enrolment

In order for your pension provider to know which of your enrolled employees to contact, you must provide them with the details of who is enrolled with them such as their name, date of birth, address and assessment result.

Employee Pensions

The Pensions Regulator requires that you send information to them about how many of your employees you have enrolled. Clear Books Payroll enables you to send details about the employees who you have automatically enrolled and which pension scheme(s) they are in as part of your Declaration of Compliance.

Pensions Contributions

You will need to give updates to your pension provider each time you deduct pension contributions from your employees. You can use the pensions contributions report to see details of a specific pay reference period for each pension scheme.

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