Filed for extension but cannot complete taxes in software

Hello,

 

I had a situation of overcontribution to Roth IRA accounts. It was taking a while for brokerages to recharacterize funds and hence I filed for extension on April 13. It was approved on 14th and required payment was debited on 16th.

 

Now I'm ready to complete the taxes in software. I do owe the IRS but considering payment made with extension, I should get a refund. 

 

How do I tell the software about payment made with extension?

 

Thanks