The present invention provides an automated material handling system (AMHS) having: a FOUP management system, for managing a plurality of multiple lot FOUPs; a real time dispatch system for controlling dispatching of wafer lot orders within a wafer fabrication system; an automatic material handling integration system having a stocker for storing and sequencing a plurality of FOUPs, the stocker having an embedded sorter disposed there within for sorting wafers within a plurality of multiple lot FOUPs, and a FOUP transportation system for transporting FOUPs within a wafer fabrication facility; a manufacture execution system in operative communication with the real time dispatch system for controlling recipe processing and for controlling flow of FOUPs within the FAB; and a computer integrated manufacturing system for automating equipment within the AMHS. Additionally provided is a methodology for using the embedded sorter to sort FOUPs and a plurality of wafers within the AMHS.