Speical Order & Back Order Distinction

In my business we have a regular inventory of items we stock... but what we carry is only a portion of what we can offer.  I would like to sell these items... but I want my customers to know that there is an extra waiting period for these items (which is approximately a week).

My issue is that occasionally the items we carry in-stock do go on back-order... and when this happens, we ship these items to the customer for free... we often have to split the order into two shipments when this happens.

But when a customer orders a special order item (an item we do not stock), and they want their order shipped in two shipments just so they can get their in-stock items right away, I want to charge them extra for shipping.  My issues is, I want this to be clear during through out the whole process that this is how things are going to go.

We are going to post this information everywhere, so it should hopefully be obvious, but I still want an extra distinction made...  Is it possible to ask them when they are going through the checkout process if they want their shipment shipped in two shipments.. and we will add on an extra shipping charge after the fact?  Can I easily add an extra question or two in one of the steps?

Cool, thanks for your help.  I have done everything that you listed.  My only concerns are to better distinguish back-order products from special-ordered ones, as we have different policies regarding both.  I think if we put *special ordered item* in the title of each product that is special order only, this will probably do the trick.