Once you have EFiled, do not refile the tax return if it has already been Accepted. You actually wouldn't be able to refile a new Form 1040 because once your Social Security number has been used for EFiling, it is locked for the remainder of the filing year.
You stated you had a Form 1099-NEC & two Form 1099-Ks. When you say you "reported all of them", but forgot to add the Form 1099-NEC on the Schedule C, does that mean you did not report the income stated on the Form 1099-NEC? If you included ALL YOUR INCOME from all three 1099s, you will be fine. If you made a mistake, you can always file an Amended tax return to include all your income.
As for paying any taxes owed, there were/are multiple options. You could've had them withdraw from a bank account, you could pay by mail with a Voucher or pay through your account on IRS.gov, if you have one.
