Assuming you have set up Head Office Customer Account and Branch Office Customer Account.
You can create, print invoices to the Master Customer Account as well as Branch Office Customer Account using Normal Invoice processing method.
The only difference is if a Branch Office Customer Account is selected, a "Branch Indicator Icon" will appear next to the Customer Field at Invoice Creation Screen.
However, you will not be able to process Payments from the Branch Office, you will not be able to create a batch from Branch Office Customer Account.
When you print AR(customer) Statements or perform customer enquiry, all branch invoices and credit notes will appear on the head office statement. Invoices and credit notes pertaining to that particular branch will appear on that specific branch office statement.
Not to worry, there will not be double posting to the same GL account.
For information on setting up linked customer accounts on head office / branch basis see this earlier blog post: Customer Accounts on Head Office or Branch Basis