Super Orders only appears to support one kind of back order: where one or more items in the order are out of stock. Then you can use the 'edit products' link and split the order to create a new order for the back ordered items. If you are using a credit card gateway or PayPal you want to have it set to "authorize" only so that you can adjust the amount of money captured for the items shipped and then capture the balance when you ship the back ordered items.

If you need to back order a partial quantity (e.g. they ordered 10 but you only have 4 in stock) or you need to substitute one item for another, Super Orders won't do this. In theory the Edit Orders mod would let you do this but from my experience it does NOT work together with Super Orders. It also does not handle products with attributes properly. You can use the "Encrypted Password" mod to log in 'as the customer' and create a new order, but processing the charges gets a little trickier.

hope this helps