Did the IRS ask you to amend? You should not amend until the first original return was done processing and you got the first refund. If you didn't get the first refund you need to delete it from the amended return.
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.
Go by the actual 1040X. Line 18 should be your original refund amount and line 22 should be your additional refund. If you paid on your original return it will be on line 16. If there is an amount owed with the amendment, it will be on line 20.
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.
If your refund went down you owe the difference, because 1040 and 1040-X are processed separately.