Minor spoiler
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They are only used after you kill the vampire. When enough damage is done to a vampire it will retire to its coffin to rest. You need to use the stakes on the coffins. They are not equipped as a weapon. They may go into the quick item spotor they may be used automatically from inventory, i don't remember. However you will know when to try and use them if when you scroll over a coffin you see a sword denoting the attack cursor.
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Balance