IRS has the payment info from the first return so check the amended box and change whichever lines need to be changed. Be sure to include a statement explaining the changes and send a check for the difference in tax if you owe. The amended also has to be mailed so I'd include a copy of the first return that shows the amount paid on that return circled in red.
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.