If you are setting up a new Shogo Account, Shogo will guide you to "Create a Company" after you connect your first store.  A Shogo "Company" represents a connection to a specific instance of an accounting system such as QuickBooks Company A, or NetSuite Sandbox B.  If you need to setup new/additional companies, you can do so by navigating to Settings>Companies>Add Company

After selecting your Accounting System, follow the preceding on-screen connection steps.  To see all the accounting connection guides, Click Here.