The game will tell you when you discover a Magic Plant. You will see a pop-up message that tells you which Magic Plant you've discovered and what its benefit is. The plant will automatically be placed in a golden pot and put into the center section of your nursery (on the sell screen). You can continue to breed more of that type of plant, but they will not look "special" in any way - only the first plant of each kind of Magic Plant is put into a golden pot.