Sales Order Totals contains two sections. "Order Total" and "Shipping Total". Depending upon which section you input fees (ie manual freight, insurance, handling), how those fees are past into Sales Invoices will differ according to which series of steps or processes are used to arrive at an invoice. Please refer to the PDF link below for a detailed review of the various processes and the impact upon the Sales Invoice.
Inbound freight billing using Totals screen Insurance Fee field.pdf