After you file

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.