Go to Crow's Nest, at the end you should find a waypoint shrine, near it is the Forgotten Crypt, which the Engineer who resides in it, one of the being who holds the item that gives the Red Orb's clue, The Engineer's Sword. You have defeat him in order to get it. After that go through the wooden gates behind where you will be in the Academy, the orbs are all over the place. You have to defeat the undead (mind read him first) at the basement in order to get the Helm of Secret, which lets you see the hidden secrets of the place, which includes the orbs. The rest, figure them out yourselves.