I would either create anitemized orderfor each company so that you can add a comment in the "other costs" section as well as their outstanding balance. Or if you don't want to use itemized orders you could create a product called something like "outstanding balance" with a number attribute (which allows you to put in a value that correlates to the cost) so that you can create an order with this one "product" and add the amount they owe. Either way you'll have to create an order for each company so that they have an invoice to pay. Let me know if you need more guidance on this!
