You'll enter the amount you paid with the extension by clicking on the Federal Taxes tab (or Personal tab if working in TurboTax Self Employed), then Deductions & Credits, then scroll down to Estimates & Other Taxes Paid and select Other Income Taxes.
You'll land on the Other Income Taxes screen where you'll see Payments with Extension. There are categories for federal, state, or local payments. Select the appropriate category and enter your amount.