Can we set up payroll direst deposit for all three of our stores with one EIN number? We each have our own QB licenses account

If you have one EIN that means you have one payroll for reporting purposes, so in general that entire payroll should be in one company file so that you can then create tax forms correctly from it.

To answer your question, though, I don't think you can sign up for DD for multiple payroll accounts (you'd need to) using the same EIN.

Hi there, @Audrey81. 

Welcome to the Community. Setting up payroll direct deposit for all three of your stores using the same EIN may cause errors as QB Desktop payroll can only support one company file per EIN. 

You can have multiple firms with separate company files, different EINs with direct deposit on the same DIY Payroll subscription. 

Read through this topic: Requirements and limitations in this help article for your reference: Add an EIN to existing Payroll Subscription. 

To guide you with a direct deposit set up, refer to this article: Set up direct deposit. It includes answers to frequently asked questions about DD. 

Feel free to message again if you have additional questions. We're always delighted to be your QuickBooks guide.