The customer is not invoiced until the order is fully shipped. Shipments are not invoiced as they are dispatched. The order is regarded as being ready for invoicing only when all lines on the order have been supplied. When the orders is fully supplied one invoice is generated for all shipments.

You will have to set the customer to "Invoice Per order" before commencing.
  1. From the Navigation Panel click "Cards".


  2. Highlight the customer and Click "Settings" "Customer Settings".


  3. From field "Invoice Mode" select "Invoice Per Order"
     

  4. Click "Save"
     

  5. Create a "Sales Order" for the customer.
    Orders

  6. Create as many "Shipments" required for the order.
    Shipments

  7. Once the order has been fully shipped an Invoice will be created for the Customer order.