Payroll taxes are accrued due to labor records(time cards) being created for an employee in a particular tax jurisdiction (location) and Vertex computing the taxes relating to the location. Employers have the opportunity to enter selected override tax rates for employer taxes (generally not for employee taxes). Your AAIs in payroll have nothing to do with calculations of taxes, the AAIs only direct the resulting costs to specific accounts.
You need to examine the Tax Area Information in your system along with the Rates and Overrides in your system. These can usually be found on the Taxes and Insurance menu under HCM Setup menu. Selected employee taxes may be "turned off" by a number of employee specific settings (exempt from FICA) as an example.
Without more specific information that is the best answer I can provide.
