You must configure the switch ports that connect the ISL (these are the E-Ports). The procedure you use depends on which switch you are using.
Configuring the E-ports on the Cisco FC switch
You must configure the FC switch ports that connect the inter-switch link (ISL). These are the E-ports, and configuration must be done for each port. To do so, you must calculate the correct number of buffer-to-buffer credits (BBCs).