If you use the same exact account you used to file the extension with, you'll see what you paid already included in the Estimates & Other Taxes paid under the Deductions & Credits tab, when you get to that point in the program. If it's not listed there, then you can just add it. But make sure it's not listed there first. Otherwise, even if you unknowingly double-dip, the IRS will still penalize you for the mistake.
If you paid the IRS at the time you filed your extension, then you payment only applies to your federal taxes, not your state taxes. You would have had to file an extension with the state separately, and paid any taxes due the state separately from what you paid the IRS.
