Thanks for asking!
As you described, the player draws 3 minor arcana each act. They will also draw 3 major arcana each act - one for each prompt (aka, each minor arcana).
During each prompt the player draws 1 minor arcana and 1 major arcana. Thus, you should have 3 major arcana cards (not including the shadow) to shuffle back into the major arcana deck at the end of the act. The minor arcana cards do not need to be shuffled back into the deck, as they will not be used again.
Hope that helps clarify!