This is an example of why I say to bite the bullet and get premier, premier has sales orders which are non-posting and allow you to invoice for the entire sales order or just certain items on the sales order, leaving the rest as a back order.
Since pro does not have sales orders the only way to simulate them is to create an invoice and mark it as pending. Pending invoices do not post to the financial accounts.
Bring up an invoice and select customize. Select the invoice on the left list and click edit. Select the tab “Columns” and then scroll down and find the entry on the left that says “Other 1? put check marks in the screen and print columns and then label it “On Back Order”. Click OK.
Now on the invoice those columns will appear. When you create the invoice and have 4 items (A,B,C,D) and two items are on hand but two are not and need to be ordered. Enter the qty ordered in the back order column for the item. When it comes in, change the back order number to zero.
When you go to invoice:
* IF all items are in, no problem remove the pending and print and save.
* IF an item is on back order and you are not going to charge for it. Set the qty to zero, that will cause the sales price to be zero but the back order column will still show a qty. Then clear the pending and print and save. Then create a new pending invoice for the item still on back order.
* IF you are going to invoice for the total cost and ship the back ordered item when it comes in, clear the pending and print and save. Then create a new pending invoice for the item that is still back ordered. You have to put a qty and price in there or QB tends to close zero balance invoices. Enter a note that the item has been paid for, when it comes in set the rate to zero on the pending invoice, that sets the sales price to zero, clear the pending and print and save and ship the item.

