How do you manage your Back Orders?

We are preparing to make the switch from our current software to NetSuite and are finding lots of hurdles.

Our customers often place orders for items in and out of stock. Currently (in a non-NetSuite software), we fulfill what is in stock.  We create an invoice for only what shipped and only charge freight on the items that ship. 
We hold the Partially fulfilled Sale Order as Open.  As stock arrives, we are able to run a report that lists all the Sale Orders that have back ordered items that are now again in stock.  We take that opportunity to review the order, add the shipping for the back ordered items, contact the customer to make sure they still want the item, ask if they want to add to the order, or cancel the order, etc.