Nowhere ... payments made after filing the extension are not listed on the form 1040. So if the form 1040 says you owe $500 but you already paid $200 then only send $300 with the return. In the TT program you will indicate you will mail in a check then you can either mail a payment (even if you efile the return) OR go online to pay directly here : www.IRS.gov/pay
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