All three, all the time a mic is needed. One becomes the primary mic, and the other two are used for noise cancellation.
As for which mic becomes the primary, it's not app-dependent, but rather use-case dependent.
In regular phone mode, obviously the bottom mic is the primary, with the rear mic used for noise cancellation. But when you switch to speakerphone mode, the phone switches between the three mics depending on where a clear, loud human voice is speaking relative to the phone, and how the phone is oriented.
Same is true for when audio recording apps are being used.
For video recording, and FaceTime: Primary mic depends on which camera is being used. Turning on the front-facing camera makes the front-facing mic the primary. Using the rear camera switches it to the rear mic.