How do I link car allowance to a separate account in the P & L ?

Hi Userhelgrit, 

Thank you for reaching out. 

I have found the following articles that might be useful for you:

Set up employee allowances

Reimburse employees' mileage and vehicle expenses in QuickBooks Online

Configuring Allowance settings for STP reporting

In short, you can find the Chart of Account mapping for Payroll settings. From there, you can map out the expense account for the car allowance.

Thank you and please let us know if you require any additional assistance.