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I filed an amendment and owed the IRS. I sent in a check for the amount with my 1040X and my original says still processing. Should I have waited until I got my return ?

 
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I filed an amendment and owed the IRS. I sent in a check for the amount with my 1040X and my original says still processing. Should I have waited until I got my return ?

Generally, yes.

If you have not received the refund(s) you originally filed for or paid taxes owed, then it would have been better if you waited until those transaction(s) occurred because the IRS and/or state department(s) of revenue may have determined the change(s) you needed to make and may not have wanted you to file amended tax return(s) and instead, may have provided instructions how they wanted you to proceed. Furthermore, TurboTax begins calculating amended tax refund(s) or taxes owed based on the assumption you already received the refund(s) you originally filed for or paid taxes owed but it does provide a screen(s) to adjust amount(s).

At this point, you should wait to see how the IRS and/or state department(s) of revenue respond. While you are waiting, you should review the Form 1040X you sent:

  • Line 16 reports "Total amount paid with request for extension of time to file, tax paid with original return, and additional tax paid after return was filed."
  • Line 18 reports "Overpayment, if any, as shown on original return or as previously adjusted by the IRS."

Thus, you should be able to determine if the Form 1040X and amended state forms you sent are inaccurate due to the timing of the transaction(s). Once the IRS and/or state department(s) of revenue respond, you may have to file amended federal and state tax returns again. Then, you should pay extra attention to those lines to accurately reflect what new amended federal and state tax returns should report. Each amended state form handles/reports amendments differently but the concept is similar. Please review the following link(s) and the link(s) embedded on the webpage(s) for more information:

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