1099 Forms and W2

During the year I sold some stock and stock options that I received as incentive compensation from my employer.  When I made the sales, my employer deducted the federal taxes due on the gain.  My employer included this income and the federal tax paid on my W2.  I also received a 1099B form.  In Turbo tax if I enter this in the W2 section and the 1099 section as income, it appears to double up my income.  It looks like I should only enter this in the W2 section and not the 1099 section.  Is that correct?  Are there any implications if I do not add a 1099 section in my return, if all the income and taxes paid are included in the W2 section?