In the game as I played it, I showed it to the necromancer: not gave it. It was still amongst my quest items, where I could use it, map it to a hotkey, etc.
If it's not there, and you are absolutely sure you completed the skull-finding-and-returning quest and didn't reload an earlier save or anything, then it sounds like you have a bug.
Try opening a save from just before you gave it to the necromancer, checking it's in your inventory first, then showing it to him again, and then checking for it in your inventory again. If it's disappeared again... then that's very strange, because I don't think it should be doing that.
If the skull is in your inventory, but does not summon a creature, then try doing the creature-design thing with the necromancer. Maybe you need to design a creature first?
If the skull still won't summon a creature, and you don't have all bodyparts (head, legs, torso, arms), maybe you need them all before you can make a creature? In which case, just keep killing things and opening chests, and eventually you'll get enough parts.
