The final bosses are spread out over the main areas of the game Mellow Hills, Heaven's Peak and your Tower.
Mellow Hills - Rescue Village
There are 3 beholders and are lethal underneath; get "above" the creature using spells, by placing green minions on the guard walkways so they auto-jump and destroy the monsters themselves or using red minions to throw fireballs, but it is only effective for 2 normal beholders, the fiery one is immune to the fireballs. Once all three of the monsters are dead, deal with the peasants.
Heaven's Peak - Kill Khan
Note, once you go into this stage, you pretty much finish the game since upon returning to the Tower, you face the final boss. As Mellow Hills, but with more beholders, enemies, and a boss trying to kill you. First part, kill the two beholders by using the raised areas near the portal. Face off with Khan (and swarm him with a green minions and drive him to the next area.
The second area has a single beholder that flies straight up to the Overlord's spawn area; use Inferno or Combust to destroy the beholder (you can also use the red minions from the nearby red portal but the spell is faster). Face off Khan who will be supported by many beholders outside of the castle; since there is no good way to battle them all, send a few minions on the turnstile to close the drawbridge, hold off the small peons and summon more brown and green minions to swarm Khan.
Losses will be heavy with the boot stomp and axe swing attacks. Recall the horde and send them out with Anger or Legion of Terror/Honor (Anger is more efficient). Follow Khan to the next area and ignore the final two beholders -- focus on killing Khan and the other enemies die instantly. The best place is the highest area with a max horde of green minions.
Tower - Kill the Wizard
Although you can still forge items and visit the dungeon for lifeforce, the other parts of the tower are off limits. The last boss is down the practice area. Head downstairs and fight off the opposing minions; once they are all dead, the wizard moves to another spot and you regain control over the brown minions and get all your spells back. Go through the door broken by the wizard and get the other nests back.
Get the red nest first (it's on the high hill trail). Operate the turnstile and get the nest back to the tower heart. Grab the blue nest on the lava to cross the water for the last nest (green). Don't forget the turnstile on the fire -- that's for the bridge to the other side. Grab the green nest in the water and use the green minions to pass the poison area. The poisoned area has a door to the wizard's chamber; be sure to use a blue or red minion to restore life and mana before heading into the boss chamber.
Use greens to jump on him and avoid his whirlwind attack. When opposing minions are summoned, defeat them in free pillage and focus on the wizard. Once the wizard is defeated, the ending spun depends solely on the good-evil alignment.