You will enter the 1099-R, and Box 2a will be the Taxable Amount. When you enter your 1099-B, you will need to adjust the Cost Basis to the amount in Box 2a.
You don't have to indicate 'Employee Stock', just check the box to adjust the cost basis.
You will end up with the 2a amount being taxed as Ordinary Income from the 1099-R, and taxed as Capital Gain/Loss from the 1099-B entry.
Click this link for detailed info on Reporting 1099-R and 1099-B.
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