Can I pay employees from more than 1 bank account if I have different branches of my business?

Hello, heather-richmond. 

Yes, you can. Just select the correct bank account when you pay your employees. However, make sure they have different pay schedule for the payroll. For example, If you want to pay employees A, then make sure all employees A are paid the same pay schedule. Then, If you want to pay employee B, then ensure all employee B are the same pay schedule.  

Otherwise, you can't pay employees on different account if they have the same pay schedule. 

Here's how: 

1. Go to the  Payroll menu and select Employees.
2. Click Run payroll, then find the employee you want to pay. 
3. Press Continue, and enter the info needed. 
4. Tap Preview Payroll, and select Submit payroll.
5. If creating a paper check, handwrite or print the check and give it to the employee by the check date.
6. Select Finish payroll.

Additionally, you can run some payroll reports in QuickBooks. This way, you can get a closer look at your business's finances and view useful information about your business and employees.

I'm just a reply away if you have other questions with the QuickBooks Online. Just add the details of your concerns in this thread and I'll help you out.