When I run the last payroll of the year do I change the salary amount to what the employee has been paid for the year?

Welcome to the Community, @thedrayessexltd.

I want to ensure we're on the same page in resolving your concern about the negative amount showing when running the last payroll of the year in QuickBooks Online (QBO).

That said, I would like some information, perhaps a snapshot showing your concern. It will give me better insight into this matter and allow me to provide an appropriate solution.

I'd appreciate any additional details you can provide. I'm looking forward to your reply. Have a good one!