There are a few ways to go about this:
1. If the order will never go on a trip
Right click on the order and mark it delivered, this will put the order into a delivered status removing it from any trip/contract boards and allow it to be audited and invoiced.
2. If the order is intended to go on a trip but needs to be invoiced
Mark the order as payment type 'C.O.D', this will allow an invoice to be generated but leaves the order in a pending state.