Dana - Some friendly thoughts here.
To protect yourself I think it's a good idea to just take a step back and scope the potential implications of this project further before you get too far. That is, verify you wouldn't be creating new problems since you're going around a system restriction which may have an underlying purpose that's not obvious yet. Maybe what you do before any more scripting is in a copy company, create an order as Standard and set the lines that way you've described, then DFDM the OrderType = B (or set the pseudo Last Invoice No) knowing the front end doesn't allow this. Then step through the whole process of printing the order, the pick sheets, shipping d/e if it exists and packing lists, invoicing the order, verifying some of the Daily Sales Reports, and updating the invoice. See if you also get errors along the way especially during invoicing (especially if there's still backordered qty) and during updating. Then go back to S/O Entry and check your back-ordered lines. Check Order History too. Then decide if you want to script further.
Having said that, maybe you've done this scoping already. I'm just mentioning because I've burned myself a few times not having scoped enough and realizing later a 9-headed lurking hyrdra was released.