From Halopedia, the Halo wiki
You'll want to secure the Power Core, so have a Hawk or two cover the repair units, and create more Cyclops in order to speed up the process. Also create a few Marines and Hawks to deal with any incoming waves of Covenant.
Be sure to build four turrets in the center of the ship and upgrade them with the Flamethrower upgrade; This will help against the Covenant infantry that will occasionally move out to the Power Core.
The 12th Black Box is on the same location as in the previous mission. Simply take a flying unit over to the left wing of the ship. As for the Skull, kill 12 Spirit Transports first, then have a flying unit check between the two southern/ lower airlocks to find it - it's not that difficult to locate seeing the small size of the map.