How do I clear a negative sales tax payable which I believe is due to credits against taxable purchases being reduced from the total tax due?

Hello there, QB User.

Allow me to share a few information regarding the negative amount in the sales tax liability. 

In the pay sales tax window, the over payment will show as a negative immediately after you make the over payment using the pay sales tax in QuickBooks. 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.

You'll need to enter a positive adjustment or an increase in sales tax using a Sales Receipt. This allows you to clear the negative amount in the sales tax payable and match them on the sales tax report. I'd suggest 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: 

1. From the Customers menu, select Enter Sales Receipts.
2. Leave the Customer field blank.
3. In the Tax drop-down, select a 0% sales tax item.
4. If none exists, click Add New and create one.
5. In the Item column, click the first empty line then select the sales tax item you want to adjust.
6. In the Amount column, enter the amount of the adjustment then press Tab or Enter.
7. Click OK when you receive the message "Changing the amount of a tax line item may cause your sales tax reports to be incorrect."
8. Repeat steps 4 to 6 for any other sales items to be adjusted.
9. Click Save & Close.

This will move the money into or out of your sales liability account. 

I found a helpful article for more insights about sales tax adjustment: Process sales tax adjustment.

The steps above will help you clear the negative sales tax payable amount in QuickBooks. Please let me know if this works when you get a chance to try it. If this wasn't what you needed, any details you can share that would help me understand the situation would be appreciated.

How are you processing "credits?"

Example:

You don't split taxes paid from cost of purchases at all.

Or, you are allowed to track them, because you should not need to pay them at all, but cannot submit a reseller or wholesaler permit? So, you track it as your Expense. Then, in the Sales Tax function for Pay Sales Tax, you use the Adjustment function here, and flow that to the same Expense account.