Its not a stupid question :). Crystals have a natural vibration to them. Which are used for a huge variety of things, some not even associated with spells or healing. Like quartz watches and electronics...
Crystals, have been used for centuries as source for attuning your chakras and aiding in meditation. Each type of crystal has a different use and natural power to it.
The skull has power if you give it power. I think if its adorned with the crystal as a necklace, it is probably just a trinket.
But, if it were me, i would cleanse it with sea salt and re-charge the crystal at the next full moon and with your positive energy to be on the safe side.
Good luck on your new journey... :)