Or do you mean you filed the extension using the online version and are using the downloaded one to file the return ?   

If you made a payment when you filed the extension, just make sure TurboTax ultimately gives you credit for the payment.   It may populate the payment automatically for you.  If it doesn't, you can enter it (or check on it) as below:

To add, change or delete a payment made with an extension request -

• Click on Federal Taxes (Personal using Home and Business)
• Click on Deductions and Credits
• Click on I'll choose what I work on
• Scroll down to Estimates and Other Taxes Paid
• On Other Taxes Paid, click the start or update button

On the next screen, scroll down to Payments with Extension

                          

Once you have entered (or confirmed if pre populated) the extension payment, then before filing verify that you are getting credit for it.  Look at Line 70 of your Form 1040 and verify that the Federal figure is correct.  A state extension payment is entered in the same navigation steps as above.  

To get the amount paid on a state extension to show up on the state return……
When you are done updating your federal return, you need to transfer the new federal information by going back through the state tab and the state return. Nothing will change until you transfer the fed info to the state again. If applicable, verify that it appears on the state return.