I added a large amount I paid with my extension but the tax penalty stayed the same as before I added it.
That might be for not paying it evenly during the year.
You might be able to eliminate it or at least reduce it. You can go to Federal Taxes tab or Personal tab, under Other Tax Situations and select Start by the Underpayment Penalties. You will answer a series of questions that may reduce or eliminate the penalty. Or you can elect to have the IRS figure the penalty for you. It's form 2210.
It's under Federal or Personal (for H&B version) Other Tax Situations Additional Tax Payments Underpayment Penalties - Click the Start or update button
If you have the desktop program you can switch to Forms Mode (click forms in the upper right (left for Mac)) and open the 2210 form.
ps....I had a refund once and still had a penalty for not paying in evenly during the year.