If the employee's information was set up correctly throughout the year and all income was reported properly, it is likely you simply need to click the Recalculate All button on the W-2 Forms.
If the employee's taxable income was not reported as taxable when each paycheck was issued, you may update the records. Logos Accounting has a routine called Edit Payroll Check History, which allows you to change information for tax forms without posting anything to your ledger. This routine works by employee, by paycheck.
Select Payroll, Employee, Edit Payroll Check History.
All employees will display. Highlight the Employee whose taxable record you need to update and click the Checks Tab.
Highlight the check for which you want to update the taxable wages information and click the Tax tab. You will do this for each check you need to update.
In the Employee Wages Column, update the Taxable Wages to the correct figure.
Click Save and move to the next check until all checks have been updated.
Once you have completed updating each check, go into W-2s, scroll through until you find the updated employee, and then click the Recalculate button at the bottom. This will update the W-2 for that employee with the current information.