In Auto or Manual mode, activate the Settings menu from the top right corner of the app.
Under My Tunings, tap on Custom Tuning to add a custom tuning.
From here you can select an instrument, name your tuning, and set a note for each string. You can choose to view your tuning half-steps with flats or sharps by toggling the Flats On toggle on or off.
When you're done, in order to save your new custom tuning, you'll need a Fender Connect account. You'll be prompted to log in or sign up when you save.