Yes. Even though the sales of covered shares were reported to the IRS, you have to enter the sales on your tax return in order to include the gain or loss in your income. If there are a large number of covered sales you do not have to enter them all individually. You can make a summary entry for each category: short-term covered and long-term covered.
The tag below your question indicates that you are using TurboTax Deluxe Online. You cannot report investment sales in TurboTax Deluxe Online. You will have to upgrade to Premier or higher, or use any edition of the CD/Download TurboTax software.