Ammending prior year taxes, how do I get back overpayment

Hi, I failed to claim deduction such as mileage and expense on my taxes. So i owed money and i paid the irs. I am filing an amendment 1040x  and i am getting a refund after i put in all mileage and expense. But there is no section of what i have paid to get it back. For example i paid 1000 for federal and now federal owes me 2000 how do i get the 1000 back. Where do you put it on the form. Turbo tax does not ask me. Because technically i should get the 2000 plus 1000. any advise will be great.