FPS Employee Number

Hi 

We are currently using another payroll provider and are looking to implement QB Standard Payroll. Our currently provider doesn't have payroll ID's. When we submit our FPS via Quickbooks I need to ensure a duplicate record isn't produced and that HMRC don't see this as a secondary employment with the same employer. How do I update their record to say this is the same employee but with a new payroll number?

Thanks