When the supplier raise an pre-payment invoice
- I create an invoice which go on a prepayment account (or item). It's not related the real items I'll get. It's a 'deposit' item.
- A the same time, I create a credit-note to cancel it.

Then, (that's the clever bit), every payment I made, I allocate them on this pre-payment. I never allocate payment to the real order.
When the real invoice arrives, I pay it with the credit note (even if the payment haven't been made ).

Example
I have an order A for $100 and and order B for $1000

I create:
  a pre-payment A-P $100
     credit note A-D $100
    pre-paymint  B-P $1000
    credit note B-D $1000

At that point everything cancel each other, in theory I don't owe  anything to anybody.

Then the supplier wants me to pay 30% deposit of everything

I pay $330 which I allocate the pre-payment
at that point, I can see than I need to 70+700 $ to pay and I have $1100 (from the credit not) which I haven't allocated to anything.

Now, the supplier send  and invoice half of A and half of B (but I haven't paid anything yet).

I create the invoice corresponding to the delivery
  D1 $550

And I allocate the correspoding bit from the credit note , so at that point I have
        Amount     | Allocated       | Outstanding
A-P  $100         | 30 (deposit)   | 70
B-P  $100         | 300 (deposit) | 700
A-D  $100         | 50  (delivery)| 50
B-D $1000        | 500 (del.)     | 500
D1  $550          | 550              |

I can see easily that I have 770 outstanding to pay, and 550 left to be invoiced by the supplier.
One of the advantage of that method, is it decouples the physical payment from the invoice, so for example with the 30% deposit, I don't to worry about how to allocate them to the real delivery (should I consider that half of the 30% should be allocated to D1 ? etc ...).

With that I just allocate the deposit and payment to the order A pot. And allocate delivery from the A pot (the credit note).

Hope that will help,

/Elax

Thanks
Carmelo