Thanks for choosing QuickBooks as your accounting tool, @Kroeh.
I'm here to answer your inquiry about entering negative tax amount.
Did you enter the payroll data from your company as YTD adjustments? If so, there isn't a need to enter the tax amounts with a negative sign. This is because taxes are automatically recognized by QuickBooks as deductions.
The same behavior should be applied when creating paychecks. The taxes will directly appear with negative amounts under the Employee Summary section.
If you're referring to something else, please let me know. You can provide a screenshot of the results you're getting or details on how you entered the reimbursement and HSA employee.
I'm looking forward to your response.