Hello,
Did you find a solution for this issue ?
I don't know how to pay the total amount with sales taxes with this functionality (prepayment from purchase order). But you can do the prepayment directly with a prepayment journal and settle the payment with the invoice after. In this case, you can choose the amount you want with no limit.
You can find here some screenshot : vsdynamicsfinance.wordpress.com/.../vendor-prepayment-journal
Regards,
Violaine