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Buy nowI completely understand your concern, and it's indeed challenging when your employees work in two states during a single pay period, @primeidaho.
Rest assured that I am here to help you find a way to make this work effectively within QuickBooks Online.
I acknowledge the importance of running two separate payrolls for two separate states for your business. At the moment, this option is currently unavailable.
Discovering new ways to adapt to our customer’s needs is how QuickBooks gets even better. That said, I suggest submitting a product suggestion directly to our software engineers.
We have an article presenting multiple payroll reports that can be generated to accommodate your unique needs. These reports provide valuable information on your business, employees, and payroll taxes: Run payroll reports in QuickBooks Online Payroll.
If you have any additional questions related to your payroll needs, please feel free to share them with me. I want you to know that we are determined to help you overcome this challenge and ensure a seamless experience using QuickBooks Online.