In Accounts Payable, the payments are created from the invoices so you are not able to create a payment that exceeds the invoice amount. However, you can schedule two payments on the second invoice so that the first portion can be paid with the current payment.
For example, you have two invoices for $200 and receive a payment for $250.
You cannot create a $250 payment if you are only creating a payment for the first invoice. You will need to schedule two payments for the second invoice, one for $50 and one for $150. Then include the $50 portion of the second invoice with the first so that a payment for $250 can be created.