Bit of advice needed on processing a shopping cart

Jesus, why do I give my self difficult tasks!

I have a shopping cart, which includes:
qty - instore
qty - warehouse
qty - backordered

Now what I need to do in the cart is process a way that if lets say the sale includes all instore items then to process the sale.
Now for the tricky bit:
If one item is instore and 2 items are on back order, I then still need to process the payment and a deposit for the 2 on back order.
Is there a way of processing this in a flow? or is there going to be a better way of doing things?