You should have paid those separately. Since the income tax deadline was extended a month beyond the first quarterly tax payment deadline (May 17, and April15th) it’s likely that you missed the deadline. I doubt you’ll get a penalty. But it would be wise to create a tax account at IRS.gov and check to see when that credit is applied. It could take a while. But the IRS has bigger things to worry about than your quarterly estimated payment –especially if it gets there before year-end.