Solved
On the paper I printed out it states mail check or money order. When I click more about my refund under federal return it shows my fixed amout.
No, the amount owed will not come directly out of your refund, the IRS will send you the original refund amount, and you will need to file your amended return by printing it and mailing it, along with the amount owed in order to file the amended return and pay your tax owed.
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