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Yes, you're right. Since QuickBooks doesn't allows you to assign multiple states under an employee profile, you'll have to process it manually. This means that you need to switch the states manually the moment you create payroll for the employee's working hours.
Firstly, you'll want to change the state of your employee's profile. Here's how:
After changing the employee's state, the system will use the assigned state to calculate taxes when you process payroll.
Just in case you want to learn more about how QuickBooks calculates payroll taxes, you can check out this article for more information: Understand how your payroll taxes are calculated.
Don't hesitate to leave a comment below if you have other concerns or follow-up questions on managing employees working on multi-state. I'll be around to provide further assistance.