The wages in boxes 3 and 5 are simply the sum of the taxed wages, the Wage Base, for all of the paychecks in the year.
To see what those wages are, run the Payroll Detail Review report. It will show you, for each tax and each employee, a line item from each paycheck showing the Wage Base, the resulting tax amount, the amount QuickBooks thinks is correct, the difference, and whether or not someone manually overrode the tax amount.