They found out during Sex. Padmè felt daring and decided to slip a Finger into his glorious Butt while being fucked by him or giving him head, and his reaction definetely suprised her - He was absolutely into it.

I want some nice sexytime with Anakin enjoying buttstuff with Padmè. Maybe He wears a buttplug while fucking her, maybe she just fingers him till He Comes with his dick untouched - it's up to you