I'm here to provide the help you need and guide you figuring out the negative amount in your sales tax window.
In the pay sales tax window, the over payment will show as a negative immediately after you make the over payment in QuickBooks. To better isolate this issue, let's try reviewing all the transactions linked in the pay sales tax window to see if you made an over payment transaction.
If there is, you can enter a positive adjustment or an increase in sales tax using a Sales Receipt. As you make sales, the sales tax collected reduces that negative amount until it gets to zero. Then, it will start showing a positive amount since the amount you owe less the over payment.
This also allows you to clear the negative amount in the sales tax payable and match them on the sales tax report. However, I'd recommend consulting an accountant for specific suggestions on how to adjust the sales tax liability in QuickBooks.
Here's how you can enter the positive tax adjustment:
From the Customers menu, select Enter Sales Receipts.
Leave the Customer field blank.
In the Tax drop-down, select a 0% sales tax item.
If none exists, click Add New and create one.
In the Item column, click the first empty line then select the sales tax item you want to adjust.
In the Amount column, enter the amount of the adjustment then press Tab or Enter.
Click OK when you receive the message "Changing the amount of a tax line item may cause your sales tax reports to be incorrect."
Repeat steps 4 to 6 for any other sales items to be adjusted.
Click Save & Close.
This will move the money into or out of your sales liability account.