QuickBooks can track more than one state income tax per employee if the employee was transferred from one state to another. This article explains how to track multiple state withholding.

You are not using Assisted Payroll service.

You will track multiple state and local taxes for an employee who worked in one state and then transferred to another.

Multiple State Withholding

QuickBooks can track more than one state withholding tax per employee if the employee transferred from one state to another; however it cannot track two state withholdings if the employee works in two states simultaneously.

Multiple Local Income Tax Tracking and Reporting

QuickBooks can record two local taxes on Form W-2. You must set up those local taxes as deductions with the Tax Tracking type set to Local Income Tax and Secondary Loc. Tax. Note: Both local tax types are reported in box 19, Local Tax, on Form W-2; however, Secondary Loc. Tax is not reported as income in box 18, Local Wages. According to the IRS:

"If necessary, you can issue more than one Form W-2 to an employee... If you issue a second Form W-2, complete boxes b,c,d,e and f with the same information as on the first Form W-2. Show any additional items that were not included on the first form in the appropriate boxes. Do not report the same Federal tax data to the SSA on more than one Copy A."