How to apply cash paid on behalf of other customers?

Dear All,

I am looking for a solution where a company supplies medicines to public hospitals (the customers). The customers make orders up to an allowed threshold and they must be billed the value of the order. However the customers do not pay the invoice value because this is already paid for by the government and/or donors to the supplying company.

How can the supplying company apply the funds received from the government to the invoices billed to the hospitals to close the open invoices in Oracle AR. There are over 3000 hospitals, multiple orders and about 4 deposits received from the government as payments related to the invoices.