In VC I never seem to run out, ok occasionally as I do have a life too but in PC I get two and then have to wait days for another couple!
Once you have killed a Boss you have to wait for the Boss to regenerate. With each location that you unlock, another Boss becomes available. It is the same process for each game. You are also able to join in on your Clan members's Boss Battles when you have none ready to attack.
