The amount you paid with the extension should be included already, under the Deductions & Credits tab in the Estimates & Other Taxes Paid section. If it is, then the amount shown for what you owe, is how much additional tax you owe.
If what you paid already is not included in the Estimates & Other Taxes Paid section, then you need to work that section through and add it. After you add it, you need to work through the "review" section again, so the program can "do the math" and account for what you added.
