As you are not using Simple delivery, this should be very easy as it is exactly as it always was.
If a buyer buys several items, they should not try to pay. You go to one of the items and in drop down menu select send invoice. This will bring up all BUT it is up to you to edit the postage.
Do not assume that automatic invoices will be sent, as only you know what postage is to be charged, based on weight, size and value of items to be sent.