Sales Order One Item Two Bins Problem

In QB we have a Sale Order that has one item on it, but the item is in two bins. When we create the invoice and associate the Sales Order with the Invoice, naturally QB thinks we are shipping the entire quantity on line one of the invoice, but  the Sales Order quantity is split between 2 bins so we select Bin A for line one of the invoice and enter the quantity. We go to line two of the invoice, but behold the association between the new invoice and the Sales Order is not populated therefore when we enter the quantity for line two on the new invoice it does not relieve the quantity due the customer on the Sales Order thus QB shows the Sales Order as open and back ordered. We've tried copy line and paste line, that does NOT retain the association between the Sales Order and the new invoice when you save the new invoice. 

We have resigned ourselves to using inventory transfer to consolidate the quantity for the item from Bin A and B to a single Bin. From there we invoice on one line only from a single bin and as such the associated Sales Order is showing as completely fulfilled. 

If there is a way to use two lines and two bin while retaining the association between the new invoice and Sales Order, that would be correct and a true reflection of the inventory movement through the warehouse to the customer. 

All questions and suggestions are much appreciated. Cheers.