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.
  1. Verify that the Vendor is setup to pay multiple invoices with one payment
  2. Schedule two payments for the second invoice
  3. Go to Banks > Print checks and record bank drafts to create the payment. The Invoices tab should show $50 of the second payment.