The program computes the tax and penalty once you enter the amounts in Box 1 and 2 and then the code from Box 7.
If this withdrawal was just from your contributions, there will be no tax or penalty assessed on your withdrawal. Any contributions withdrawn from a Roth are always tax/penalty free.
If you do have a "growth" portion to pay tax and penalty on, it will be added into your tax return and will either increase your overall liability or lessen your refund.
