A method and system of configuring a stack of switches includes configuring a switch with mapping information based on a user input flow mapping that defines destination port(s) (local destination port(s) and/or remote destination port(s)) for a flow to exit the stack. The mapping information includes any local destination port(s) via which the flow can exit the stack from the switch and an outbound stack port for each of any remote destination port(s) via which the flow can be transmitted from the switch to a downstream switch. The method further includes creating a decapsulation entry having a flow ID for the flow, wherein the flow ID is assigned to the flow and is unique across the stack, and configuring the switch with access to a decapsulation algorithm configured to use the flow ID via the decapsulation entry to decapsulate encapsulated network traffic of the flow received from an upstream switch.