1. A method of processing documents, comprising: receiving a plurality of stacks in an input receptacle of a document processing device, each stack including a batch of documents and a separator card associated with the batch of documents; transporting via a transport mechanism the batches of documents, one document at a time, and the associated separator cards past one or more sensors of the document processing device; detecting characteristic information associated with each document, and determining whether a particular document meets or fails to meet at least one criterion; providing a signal indicative of a separator card being transported past the one or more sensors; directing to at least one first output receptacle each document that fails to meet the at least one criterion; directing to at least one second output receptacle each document that meets the at least one criterion; directing a separator card to the at least one second output receptacle if at least one document in the associated batch of documents meets the at least one criterion; and directing a separator card to at least one third output receptacle if all documents in the associated batch of documents fail to meet the at least one criterion.