The default state of the unconnected pins will be high/1. Please clarify what do you mean by configure CTL pins. In the GPIF designer when you select the number of input and output signals in the interface definition tab, then the GPIF will automatically assign the CTL pins for these signals. You have some flexibility where you can select the signal and choose the appropriate IO for that CTL pin. You do not need to configure these pins in the firmware, you have to drive them from the GPIF state machine.