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. Send some cyclops to repair damaged deck guns to provide additional AA support against Spirits and Vampires.
Build turrets and upgrade some on the left side of the ship to AA, also deploy some Wolverines to assist. Later waves include Locusts so upgrade some turrets near the airlocks with the Anti Vehicle Gauss upgrade. Ready an army of Hawks, leave some to provide protection to the Cyclopses and deck guns and use the rest to take down incoming Spirits on the front deck before they can unload troops.
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.