Hi there knowell,
Thanks for reaching out about your vacation balance. QuickBooks Desktop Payroll is a great tool able to assist you in paying your employees for the hours they worked for your company. I can point you in the right direction for assistance with this negative balance of vacation remaining.
In order to know how you should be adjusting this negative balance, I recommend reaching out to the QuickBooks Desktop support team. They'll be able to assist in helping you make the right adjustments for your employee's vacation balance to be empty. You can reach them using the methods outlined in the QuickBooks Desktop software support policies.
If you have any other questions, feel free to reach out here.