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I had to file amended return and therefore have 2 1040 vouchers. Can I make out 1 check for the 2 vouchers?
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Yes. You can make one payment that is for the total amount due. You can either mail a check and include the vouchers or you can pay directly on the IRS website.
Why did you get 2 vouchers? Are they both 1040V or a 1040ES? If you amended your return you should only get one 1040V which you should ignore. You just pay the amount on the actual 1040X amended return.
You will still get the first original full refund (and keep it) or need to pay the first tax due. You should not amend or change your return until you get the refund from the original return or your payment has cleared.
The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.
Ignore any 1040V voucher that prints out and the new 1040. Those are what your return would have been if you had not needed to amend.
I did my taxes with TT - including the amended return. The reason for 2 vouchers is that I have to pay on both the original return (no refund) and the amended return which only shows what I owe for the change in 1099. A TT person walked me through the process and IRS accepted both returns without any payment.
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