I paid the balance on IRS notice via PayUSAtax. How do I submit amended return without payment? Do I select pay with check and attach the payment receipt from payUSAtax

missed a W2, got the notice from IRS, competed amendment on TT. But the amount due was missing the penalties and interest so I paid total though PayUSAtax. Now see i should have submitted payment and IRS would re notice me for the penalties. But I already paid the total including the penalties and interest.