I overpaid Tax to IRS through another CPA with Extension filing due to miscalculation by CPA. How do I file correct final return and report overpayment in Turbo Tax?

The extension was filed by CPA and paid IRS for $29,000 of Tax Due. When I checked final numbers in Turbo Tax, the Tax due is only $16000 only. 

Can I report tax payment for 2016 for 29,000 in the final tax return in Turbo Tax and get refund of 13,000 back?