Trophies use

[BB Shockwave]

Eh, as long as you have the item you get from the Academy equipped, you earn Trophies. If you want to upgrade troops in the Academy (they do stuff that frankly, followers or other NPC can do as well, like Zombie to Plague Zombie... although some that they don't, like Royal Snakes from Regular Snakes) those cost not only some gold, but trophies too. If you want to unlock level 3-4-5 units to be upgraded, or different races other then humans, that costs trophies as well.