Advanced Payment for Inventory Items with serial numbers

Advanced Payment for Inventory Items with serial numbers

Hello,

We sell equipment that we track the unique serial numbers on using Sales Orders.

We can charge the customers an advanced payment, then the balance on delivery.

We cannot figure out a way to do this in Books/Inventory:
- Cannot part invoice a SO with serial number tracking
- Cannot issue Retainer invoices as we cannot apply VAT correctly to them
- Cannot issue a separate invoice and book to the balance sheet as there seems to be no way to then credit future invoices 

Is there a solution to this? It is a big cash flow issues if we cannot do this.