IN the company i work for, we have inventory of merchandise that our customers have paid for already. So when we ship it out, we only need to invoice for shipping costs.

Currently this is the way it has been done.

1.Sales Order transaction created upon receipt of purchase request from our customer.
2.Special Order Purchase Order is created to purchase the merchandise
3. Merchandise received off of Purchase Order
4.Invoice created and customer pays for merchandise in full
5.Fulfillments created as Customer wants merchandise shipped to their clients

The Invoice before shipping preference in Setup > Accounting > Accounting Preferences > Order Management Tab > Invoicing Section is not clicked. We normally do not invoice before shipping. In a case like this, we check it on, create the invoice and check it off.