Hi Ichida,
I am not sure if we are still talking about the the service Inbound Service ManagePaymentOrderIn. This service was designed as simple upload of cash transactions to ByDesign. The service allows you to create simple cash payments (payment orders of type "Cash Payment").
You can either provide one GL account, to which the payment should be posted, or the Supplier/ Customer, where the payment is displayed as on account payment. Here is no "active" clearing from your end possible, e.g. discounts or references to invoices / expense reports or partial payments.
If your question is a different one, please let me know, what exactly you want to achieve.
Best regards
Marlene