The underpayment penalty (charged if you don't pay enough in estimated taxes throughout the year) should be accounted for in your tax due amount; if you're getting a refund, it will also be reflected in the refund (which will be less than if you didn't have the underpayment penalty). You can efile with an underpayment penalty, it's simply part of your overall tax due/refund amount.
The late-payment, late-filing, and interest penalties are handled by the IRS, but that wouldn't apply to this situation.