Question 1: When a monster attacks, an unopened magic card goes back to the box. It never comes back right?
*I've been playing that they never come back.
Question 2: After defeating a monster the magic cards are turned face-down. Do I need to mix them up? or am I supposed to begin memorizing where they are?
*I've been keeping them in the same locations and trying to memorize them to make defeating the next monster easier.
Correct, nothing in the rules suggests mixing them up. Also, doing so would eliminate one of the central mechanics of the game (memory) and make the "Help" action pointless.