You first might have to tell the program it was filed. If you efiled you have to check the filing status inside the program. Open your return and go up to menu item
File > Electronic Filing > Check Electronic Filing Status
Then save your return with the status. Go to File-Save. Oh and be sure to save your original return with another name so the amended return doesn't overwrite it and you can start over if it gets messed up.
And you should get a 1040X for the amended return. Ignore any 1040V voucher that prints out and the new 1040. Those are what your return would have been if you had not needed to amend.
The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.
And you should probably wait to amend until you get the first refund or pay the Tax Due in case the IRS adjusts your return for something.
