Any penalties you owe are included in your total tax due. You can pay through TurboTax when you transmit your return, you can write a check or you can go to the IRS direct pay site (of if your state has a direct pay if you are referring to a state penalty) and pay there. If you are unable to pay your taxes in full, you should still file by April 18th, but you can apply for a payment plan from the IRS. When you get to the end of TurboTax, prior to hitting file, it will give you the option to apply.
State rules vary so if you are talking about a state penalty, please respond and let us know.
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