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The Configure program is actually automatically started at the end of the Setup program.
You need to provide the IP address for the controllers one at a time. In case of a redundant controller provide both IP addresses for primary and secondary controller.
See also document 3BDD012560, "Getting Started", Section 2 Installation, chapter "Settings for Control Builder F", Boot EPROM Download.
Software should be updated before controller firmware,
BootEPROM download is correct way of upgrading controller firmware via configure window. The another way of updating controller firmware incase you don't find configure window or don't know controller IP ;), you can update firmware from project tree also, goto comissioning mode select conroller allocated resource,double click on node will open comissioning tab, per form initialise all and then bootstrap will update controller firmware, then you need to perform wholestation download and bring resource(controller) in running mode with upgraded virsion of firmware,
You can crosscheck upgraded firmware from controller web browser by typing controller ip address in internet browser. hope it helps to you...