First you had to mail in a 1040X amended return since there supersede is a business return process.
Next that notice tells you the original return has finally processed and you should have paid the original balance due prior to mailing in the amended return so this notice could have been avoided.
So since you did not pay the original balance due you should call the number on the notice and alert them that you did make a lesser payment when you mailed in the amended return (which could take 6 months or more to process). Also review the amended return ... since you didn't pay the original balance due line 16 should have been blank/zero.
Look at the form 1040X …
Column A should have the figures from the original return, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.
If you completed it correctly you will see an entry on either line 16 OR 18:
On line 16 should be the amount you paid with your original return.
On line 18 should be the amount of your original refund you received.
Then you will see your extra refund on line 22 OR the new balance due you need to pay on line 20.
