When you actually sell the shares, you will get a Form 1099-B to report the sale.
If you exercise ISO's and do not sell any the stock acquired by 12/31 of the year of exercise then you need to enter the exercise using the "ISO Exercise and Hold" interview. Your "source" document for this should be Form 3921 provided to you by your employer.
If you sell some or all of the stock on the same day as your exercise (for taxes) then you MIGHT NOT get a 1099-B because brokers are not required to issue 1099-B's for a "same day" sale, (though they are supposed to give you a statement with the same information required by the 1099).
This article on Incentive Stock Options has several different scenarios to help you with tax implications.
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