What you could do I guess is add 2 lines to the order, one positive, one negative, when you pay the prepayment, put that in the positive amount and pay it and then put that amount as a negative so that the net result is a lower invoice and your prepayment invoice has been reflected but that is all wrong.  The payment as Jay said in your other post is a prepayment and should be treated as such, being a reduction in the final amount due and when you raise the full invoice, you pick up the tax then.  That's when the actual liability is due.
Alternatively you raise a separate AR invoice and code it to "Prepayments" or something and then when you raise the final invoice, you raise a credit note to clear the "Prepayments" account.  A whole lot of work without real benefit.

What you could do I guess is add 2 lines to the order, one positive, one negative, when you pay the prepayment, put that in the positive amount and pay it and then put that amount as a negative so that the net result is a lower invoice and your prepayment invoice has been reflected but that is all wrong.  The payment as Jay said in your other post is a prepayment and should be treated as such, being a reduction in the final amount due and when you raise the full invoice, you pick up the tax then.  That's when the actual liability is due.
Alternatively you raise a separate AR invoice and code it to "Prepayments" or something and then when you raise the final invoice, you raise a credit note to clear the "Prepayments" account.  A whole lot of work without real benefit.