TurboTax calculates your amended tax refunds or taxes owed based on the assumption you already received the refunds you originally filed for or paid taxes owed. If you owed taxes on your original federal tax return, the amount owed should be reported on Form 1040X Line 16 Total amount paid with request for an extension of time to file, tax paid with original return, and additional tax paid after the return was filed (not including penalties, if applicable).