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Ok ... this is where it gets tricky ... first you should NOT file a second amendment before the first one has been fully processed AND you have paid the balance due on the first 1040X. If you did NOT pay the balance due on the first 1040X then line 16 of the second form 1040X should reflect all payments made to date. This is NOT something the online program can handle so since you must mail in the amended return you can adjust the line 16 if needed and recompute the rest of the return before putting it in the mail.
As mentioned, see 1040-X Line 16 and enter the correct amount to date.
This will affect the "amount you owe" on 1040-X No. 2.
TurboTax, which claims to be world class, should do better.
Amending an amendment when you have not fully completed all the obligations of the first amendment is nothing the ONLINE program is prepared to handle. If you use the downloaded program then you could switch to the FORMS mode to make the change but this functionality is not available in the online program.
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