This is easily missable in the first 2 missions of the game. In order to u lock the skulls, you have to complete a optional objective during any mission...
Mission One - Kill 100 Grunts.
This can be done on Normal, though you can do it on Heroic or Legendary if you need to. Over the course of your mission, as you're helping out and recruiting retreating Marines, you'll run into singular Grunts, packs of Grunts, or Grunts grouped with an Elite. One thing that is strongly recommended is to let Sgt. Forge and the Warthogs go for the grunts only, as they can move a lot faster by themselves or grouped together than when grouped with Marines as they will slow you down if you group Warthogs.
As you get to the gates of Alpha Base, your Grunt Kills should be at 44. Now, several pinned-down Marines will be fighting a large pack of Grunts (about 10). IF you don't get to those Grunts first and kill them yourself, the Marines trapped tehre will kill them first and you will NOT get credit for those Grunt kills. Send Forge and the Warthogs alone on ahead to wipe these Grunts out to get the kills counted towards the required 100 (with these your score should be 54 Grunt Kills).
From there, have the Marines take down the shield leading into Alpha Base and focus on the Grunts and Elites within the grounds, but keep the two groupings at the upper-right corner of the grounds alive (as once all enemies are cleared from the grounds, the Mission ends immediately).
IF you have to, send 1 unit of Marines after these groups and they will kill the Grunts first, leaving the Elites for last. When one group's Grunts all die, quickly switch the Marines' focus on the 2nd group, and when their Grunts are dead, pull the Marines back to keep those Elites alive.
Now, if your Grunt Kill count is still below 100 (say 97) then quit the mission and start over, either still on Normal or redo it on Heroic.
Once you have the 100 Grunt kills, send a unit of Marines back through the gate leading onto the grounds and have them go straight to the wall OPPOSITE of the Gate. You will find the skull waiting for pickup. Don't send a Warthog as it won't climb up to get the skull.
Mission Two - Kill 20 Jackals
This one's easier than the Mission One optional objective, as there will be more thank 20 Jackals scattered across the map. they're either on foot, in lookout towers, or on lookout points in the mountains littered across the map. Marines using grenades/RPGS, Forge in his Gauss Warthog, and Scorpion tanks can easily waste the lookout Jackals quickly.
Once you get your 20, send a Warthog back to Alpha Base and check the lower lefthand corner for the skull.