There are two ways to do this:
Option 1. Go to Sales → Sales Transactions, click Plus and select Invoice.
Once you've chosen the customer, you will see a side panel with a list
of all open sales orders (if the customer has any). Mark one or multiple
orders and click Add. When you are finished with the invoice, click Save.
Option 2. Go to Sales → Sales Transactions and find the sales order you would like to invoice. Select Create Invoice in the Actions column. On the New Invoice page you will see a side panel with a list of other open orders (if this customer has any more). You can mark them and click Add to include them on the invoice. When you are finished with the invoice, click Save.