Use the Company from the BILL TO address, NOT the company from the SHIP TO when you post checks. The BILL TO company is always the one that pays the bills. In our system, it is usually different as we primarily ship to schools and are paid by the school district. Thanks.
For clarification, this request pertains specifically to the Pay Name field that auto-populates in Apply Payments as seen here - http://screencast.com/t/kwYfQRxInk