An amended return cannot be e-filed, it must be mailed. When you go through the amendment interview, it should ask what you received with your original return (refund) line 18 of Federal 1040-X, or what you paid with your original refund, line 16 of Federal 1040-X form. Then the program will calculate the refund or payment paid and will show an additional refund due Line 22, or an additional payment owed line 20.
If your original return has not been fully processed, you should not amend your return yet.
