You could split up the the number of shares exercised on your Form 3921 into two or more entries, although you are not required to enter this into your tax return filing.
You don't "enter it on your income tax return" in the sense that the IRS will receive the Form 3921 as part of the income tax return itself, but you might want to enter it in TurboTax when you do sell the stock if you use the ISO "Guide me" interview because that's how TurboTax helps you determine the correct basis to use.
However, if you know the correct basis to use for the sale - which is not the amount reported by the broker on the 1099-B - then you don't need to enter the Form 3921; you simply enter the 1099-B as it reads and then tell TurboTax you need to correct the basis.
Click this link for more info on Form 3921.