If it was a campaign skull basically when you start a campaign mission, there should be an option to activate skulls that you have found/unlocked. These skulls have different gameplay affects, majority of them make gameplay harder and give you point bonuses
for when you are playing the metagame (so this is useful for attaining the metagame acheivements). If you want to go for the metagame achievements, i'd recommend finding/unlocking majority of the skulls, you can find videos on youtube of all skull locations.
If it was a skull on a multiplayer (mythic) map then it doesn't do anything apart from unlock achievments and contributing to a vidmaster achievement.