You enter them both separately in the Retirement income section....after you enter the first one, and answer a number of follow-up questions, you will either be asked if you want to enter another...or will be shown a table of 1099-R forms already entered, and you can hit a button to "Add Another 1099-R"
Both 1099-R forms will be entered in the income section of your return. The total of the distributions should equal the amount that you received. If taxes were withheld, the amounts should equal the total of federal and state taxes. Next year will be easier with only one 1099-R from your pension.