When Bristling Hydra enters the battlefield, you get {E}{E}{E} (three energy counters).
Pay {E}{E}{E}: Put a +1/+1 counter on Bristling Hydra. It gains hexproof until end of turn.
Energy counters are a kind of counter that a player may have. They're not associated with specific permanents. (Other kinds of counters that players may have include poison and experience.)
Energy counters aren't mana. They don't go away as steps, phases, and turns end, and effects that add mana “of any type” to your mana pool can't give you energy counters.
If an effect says you get one or more {E}, you get that many energy counters. To pay one or more {E}, you lose that many energy counters. Any effects that interact with counters a player gets, has, or loses can interact with energy counters.
Keep careful track of how many energy counters each player has. You may do so by keeping a running count on paper, by using a die, or by any other clear and mutually agreeable method.
You can't pay more energy counters than you have.
{E} is the energy symbol. It represents one energy counter.