No, you only want to enter the cost basis of the stocks that were sold as the cost basis.
If you only sold the shares to cover the taxes, the adjusted cost basis you should use is the basis for Y that Fidelity reported in its supplemental information. The information in box 12 of your W-2 pertains to the total shares of NQSOs received, not just the ones you sold.
For more information on the tax treatment of NQSOs, see this article.
