I’m exempt from workplace pensions duties as a director and only employee in the Ltd, confirmed with HMRC. How do I add this to the system so I can run the Payroll?

I'll provide two scenarios to address your concern and help you update the payroll system to reflect your exemption from workplace pensions, Aniko.

If you haven't set up your workplace pension, choose the Company Director option in the Tax Info section. It will categorize you automatically as Not Assessed for your workplace pension. I'll show you how to do this:
 

1. Navigate to Payroll, then select Employees.
2. Select your profile from the list of employees.
3. Click Edit in the Tax Information and check the Company Director box.
4. Set the Appointment Date and choose the Director Calculation Method.
5. Click Save.
6. Go to Workplace Pension, Loan & Other Deductions and click Edit.
7. In the Pension status, the Pension scheme will show Not Assessed. After that, hit Yes under Exclude from Pension from the Advanced dropdown menu, then tick Done. 

If your workplace pension is already set up and deductions have started, you can choose to cease the membership. Here's how:
 

1. Go to Workplace Pension, Loan & Other Deductions and click Edit.
2. From the Pension Status, toggle off the Enrolled in Pension button and select Cease Membership.
3. Set the Reporting Date and click Save.

You can scan this article for more process handling workplace pensions in QBO: Set up and manage workplace pensions in QuickBooks Online Core Payroll.

Ensure you maintain a payroll history to help you verify employee payments and track your company's salary expenses.

I'll keep this thread open to ensure you get timely help with your workplace pension in QBO, Aniko. Remember that the Community forum is always ready to assist you.