When you enter the 1099R there is a spot to enter the tax that was withheld.
To enter your retirement income, Go to Federal> Wages and Income>Retirement Plans and Social Security>IRA 401 k) Pension Plan Withdrawals to enter your 1099R.
You had tax withheld from the distributions from the retirement account, just like when an employer withheld tax from your paychecks. When you enter it all into the software, the calculations are done to reconcile the amount of income you received and the amount of tax that was withheld. You might owe more or you might get a refund.