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The discount amount per share for a qualified employee stock sale will be the discount percentage times the market price on the grant date. You would multiply that times the number of share sold to determine the discount applicable to the shares you sold.
On the screen where you enter the investment sale, you will see an option to indicate that the cost basis is missing or incorrect:
As you continue through that section, you see an option to enter the correct cost basis:
If you know the correct cost basis, once you enter it that is all you need to do for that stock sale. The discount should be reported on your W-2 form as wages in box one, and once you enter the correct cost basis for the Form 1099-B reporting, you have accounted for the capital gain.
When you are done with that section, you will see an option to Add more sales:
