Minister of Inquiries

Keep track of how many energy counters each player has. Potential ways to track this include writing theme down on paper or using dice, but any method that is clear and mutually agreeable is fine. (At higher levels of tournament play, dice may not be allowed for tracking counters that players have.)

Energy counters are a kind of counter that a player may have. They're not associated with any specific permanents.

Some triggered abilities state that you "may pay" a certain amount of {E}. You can't pay that amount multiple times to multiply the effect. You simply choose whether or not to pay that amount of {E} as the ability resolves.