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1. You should fill the PortPin Mscr value for each pin you have configured in Pins Tool. Since RTD 6.0.0 this step is not necessary. it fills automatically.

2. Regardless of the peripheral configuration in Peripherals Tool. If such signal are routed to an external pad, then it is needed its respective configuration in Pins Tool.
3. You just add them, Update Code and write in main file its respective include.
4. For interrupt configuration use the IntCtrl_Ip driver.
I hope this information is helpful.