We have multiple checking accounts for different entities within our organization, and sometimes the default bank account set for a vendor isn't applicable. It would be helpful to be able to select the bank account when entering an invoice, especially since most users will not have rights to go into an open invoice and edit after submission. Even more helpful would be the ability to split an invoice across multiple bank accounts.
I completely agree that check processing needs to be streamlined for companies that are working more than one entity in the database.