All you need to do is right-click with it in hand and it will subtract your points directly into it. You’ll see the level bar below it indicating how much is contained within it and it will glow after the first point is added to it.
You can also hover over the icon in your inventory to see just how full the gem is. And you can easily get that experience back by shift+right-clicking with it in hand. Use this item to safely store your XP for later use or you can give it to other players if you’d like to share it!