A Qualifying Disposition would be when You sold the stock at least two years after the offering (grant date) and at least one year after the exercise (purchase date). A Non-Qualifying Disposition would be when you sold the stock within two years after the offering date, or one year or less from the exercise (purchase date).
Your Cost Basis per share would be the Exercise Price per share, plus the amount of your discount that was added to your W-2, divided by the number of shares you sold.
For example, if you exercised and sold 100 shares, and $1000 was added to your W-2 for your discount, divide the $1000 by 100 ($10) and add that to the Exercise Price per share (let's say it was $50), so your Cost Basis per share would be $60 when reporting the sale on a 1099-B.
Once you know your Cost Basis, you can enter your 1099-B as a regular stock sale (don't indicate employee stock, as that takes you through an interview to help you determine your Cost Basis), and check the box that says 'my cost basis is missing or incorrect' and enter the correct Cost Basis on the next page.
Here's more detailed info on Employee Stock Purchase Plans that also discusses Qualifying/Non-Qualifying issues.
@RHS4
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