You enter the amount that you know is correct. If the income reported on the 1099 is lower than the amount you have recorded throughout the year, use your numbers.
Remember, the 1099s are not sent in with your tax return. The IRS will attempt to reconcile the 1099s they received in your name (or business) to the amount you report. If the total of the 1099s they received are less than what you actually report, they will use your numbers. However, if the total of the 1099s they received are more than what you actually report, then you'll get a notice asking why.
