Thanks for reaching out to the QuickBooks Community, vrtllc.
I'm here to ensure you have all the information you need to pay your employee working in two different states.
You can edit the employee's work location in their profile before running payroll. Regardless of whether it's within the same timeframe or not, process the payroll for the first state, then modify the employee record to reflect the second state as the place of work and issue the second paycheck for that pay period. If using schedules, run the second check as an unscheduled payroll.
Here are the steps to make changes to your employee's work location:
Navigate to the Payroll tab, then click on Employees.
Choose your employee.
From Employment details, click on Edit.
In the Work location dropdown, you will find a default work location (typically your company's address). You can select an existing address or click +Add work location.
If you opt to add a work location, input the physical address where your employee works and select the correct address from the list. Avoid using a P.O. Box. Providing the physical address helps us determine the correct taxes.
Furthermore, you can take advantage of the payroll reporting functionalities in QuickBooks. These reports empower you to handle payroll taxes and conveniently track employee expenses.
If you require further assistance paying your employees or related matters, reply to this thread. I am here to support you at any time.
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