Welcome and thank you for reaching out to the Community, dkutej.
At this time, QuickBooks Desktop Payroll can only support one data company file per EIN. Trying to use multiple company files with the same EIN and payroll subscription might cause errors when doing the task.
Here are some articles you can check on how to pay and file taxes in QuickBooks Desktop:
Please let me know if you have any other concerns. I'll be around to help you out.