Heretic Skull - From the centre of the ship, turn to face the blue tinted section and fly up to vent on the right. Switch back to a Spartan using the D-Pad and quickly catch the skull before you fall past it.
Citadel - Again from the centre of the map, turn to face the powerup in the blue tinted section, from here turn left to face the wall in the adjoining room with the blue panneling. Spawn a box and a grav lift and then use it to launch yourself as a Spartan into the small hole at the top of the support beam to grab the skull.
Longshore - Fly out over the water, and while facing back into the map turn left and head towards the air vents on the side of the warehouse to find the skull tucked neatly behind them. Switch back to a Spartan using the D-Pad and quickly catch the skull just in time to fall to your death.