You will pay income tax based on whatever your W-2 says. If your W-2 is incorrect, you will need to get it corrected with the payroll company. Or, request the that the checks be re-issued so that your W-2 will in fact match what you were paid.
There is a procedure that you can use to file your tax return if you believe that your W-2 is incorrect. However, this will raise a red flag with the IRS. You are not supposed to use this procedure unless you have requested that the payroll company issue a corrected W-2 and they have refused. Then, if the check was issued but lost, and you have the ability to request a re-issue, the IRS may view that you have in fact been paid that money and that your W-2 is correct after all. So you should make an effort to get the situation straightened out before you file your tax return.
