Mana is what you collect as you make matches during battle. Every match of 3 will gain you one mana stone from the element you matched. Every minions ability will require anywhere between 2 and 8 mana to activate.
Your pedestal will help you see what type of element you need to match, and how many matches you need.
When making matches and earning mana during battle, the mana will always go to it's corresponding pedestal regardless of the elemental preference of the minion equipped there. For example: if Flint, who has a strong affinity to Fire Mana Stones, is equipped to the Wood pedestal, his ability will be charged by Wood Mana Stones.