How do I file and pay when I asked for an extension

When you requested your extension you were supposed to pay your estimated tax due.  Did you enter the payment you made into your tax return? 

Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes 

You don't have to do anything special. Just file and pay as you normally would, the same as if you did not have an extension. But if you made a payment with the extension, make sure that payment is entered in your tax return. See the reply from xmasbaby0 above.