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 

To enter the amount you paid with an extension for Federal & State:

Federal Taxes (or Personal for H&B/Self Employed version)
Deductions and Credits
Scroll down to Estimates and Other Taxes Paid
Other Income Taxes - Click the Start or Update button
On the section Payments with Extension
Either Visit All or Click Start or Update by the extension you paid

When you are done entering the payment for State, then go back through your State interview so the information from the Federal return will transfer to your State return.