No, do not include the stock that was sold to cover the tax withholding on Schedule D or on Form 8949. You are correct in that your company has already included on your W-2 the withholding amount from the stock that was sold to cover. Thus, you only need to enter the stock that you sold that is reflected on your 1099-B.
Moreover, your company also included on your W-2 the value of the RSUs when they vested. Thus, your Schedule D and Form 8949 will reflect whether you had a gain or loss from the sale of the RSUs.
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