For this transaction, you only want to list the cost basis of the shares you sold. Since they were exercised and sold on the same day, the cost basis and proceeds should be just about the same number. You may have a small loss if any transaction fees were charged. In your example, the $50,000 is the cost basis of all the shares that were exercised. Since you only sold 25% of them to cover taxes, the cost basis is 25% of $50,000 or $12,500. The 75% you are holding does not need to be reported anywhere in the stock sales section until the year you actually sell them. When you do sell them their cost basis will be $37,500, 75% of $50,000.
The sales category should be listed on your 1099-B. It is definitely short-term. Covered or not is whether the basis is reported to the IRS. Usually, it is a short-term covered transaction.
