You can submit your amended return without making your payment first. You'll want to make sure you update the amended return to show that you haven't made the payment so that you can have an accurate idea of what your net refund or balance due would be.
If the additional payment that you reported was more than the original balance you owed, you should have a net refund. If your additional payment was less than the original balance owed, you'll just need to pay the difference.
