Purchase Orders - Orders received over several invoices

I have a situation where I have issued a purchase order for two new lines of stock from the same supplier and paid this in advance - thus creating a fully paid PO. 
Unbeknown at that time the supplier delivered the items separately and issued two separate invoices for these items which came in less than the Proforma Invoice on which the PO was raised.
How do I convert the order into a bill for the two separate invoices? As far as I can see I can only convert the PO once regardless of the number of items listed on the Purchase order. I would of thought that where goods/items are delivered in mutiple transactions due to supplier/production constraints that this would be a standard requirement.
I have tried converting the order into a bill against one supplier invoice and deleting the item line not applicable to that invoice but this effectively assigned the entire PO against that first invoice leaving nothing for the second invoice to be assigned to.
There is also the issue that there will be a credit balance left on the account which would be still outstanding on the PO after the two invoices are processed.
 
This is giving me a major headache so any help would be gratefully received....