I understated IRA income in 2018 1040 filing by the tax withheld amount. I filed 1040X to correct, but paid electronically. IRS refunded the payment. How do I pay now?

My IRA understatement mistake related to my wife's RMD.  She passed away on 1/15/19 the account froze and no 1099R was received from our broker.  In error I used the amount of distribution and failed to gross up by withheld tax. When I finally received the 1099R I corrected this error with a 1040X and paid electronically.  Today IRS refunded to payment.  Now I don't know how to make a payment since the return was filed without a payment attached.