Hello @chugheshci,

Thank you for posting here in the Community. I can share some steps so you can record the payment made outside the program.

Since you don't have the option to change the payment method and you've already paid through the state website, you can record the payment manually in QuickBooks. This would remove the taxes due in the Pay Liabilities section.

Here's how:

1. Click the Employees tab, then choose Payroll Setup. 
2. Proceed to step 5 (Year-to-Date Payrolls).
3. Select Continue.
4. If your company has issued pay checks this year, choose Yes, then select Continue.
5. Click Edit on Tax Payments.
6. Press the arrow next to the quarter you would like to enter tax payments in.
7. When a quarter is selected, the window will open all taxes owed within that quarter. There will be three columns: QuickBooks - Calculated Amount, Total Amount You've Already Paid, Balance Remaining. Enter the payroll tax payments you've made.
8. Once all payments have been entered for a quarter, select the next quarter and repeat the process until all tax payments have been entered.
9. Select Done Entering in Tax Payments when you have completed entering payments.

I've also attached an article you can use to update a bank account for state tax e-payments in QuickBooks: Change bank account you use to make e-payment for tax liabilities.

Drop me a comment below if you have any other questions related to state taxes. I'll be happy to help you some more.