Hi Bruce-wilson,
Thank you for reaching out to the QuickBooks Community! There are numerous ways to add paid time off to an employee. The approach can vary depending on the Payroll service you're using (i.e. QuickBooks Online Payroll, Intuit Full-Service Payroll, and so forth). This link provided includes the solutions to do so. Once you make those necessary adjustments, you should not see any negative balances. Keep me updated and let me know if you have any more questions.