The cost reduction applies only to generic mana in the total cost of green spells you cast.

You choose how many targets The Earth Crystal's last ability has and how the counters are distributed as you activate it. Each target must receive at least one counter. This means, for example, that you can't target two creatures and assign them two and zero counters respectively.

To determine the total cost of a spell, start with the mana cost or alternative cost you're paying (such as a flashback cost), add any cost increases (such as kicker costs), then apply any cost reductions (such as that of The Earth Crystal's first ability). The mana value of the spell is determined by only its mana cost, no matter what the total cost to cast that spell was.

If a creature you control would enter the battlefield with a number of +1/+1 counters on it, it enters with twice that many instead.

If the rare case where you control two of The Earth Crystal, the number of +1/+1 counters put on a creature is four times the original number. Three of The Earth Crystal multiplies the original number by eight, and so on.

If two or more effects attempt to modify how many counters would be put onto a creature you control, you choose the order to apply those effects, no matter who controls the sources of those effects.

You don't choose a target for Eden, Seat of the Sanctum's last ability at the time you activate it. Rather, a second "reflexive" ability triggers when you sacrifice Eden, Seat of the Sanctum this way. You choose a target for that ability as it goes on the stack. Each player may respond to this triggered ability as normal.

If one of the creatures is an illegal target and the other one isn't as The Earth Crystal's last ability tries to resolve, the original distribution of counters applies and the counter that would have been put on the illegal target is lost. It won't be put on the remaining legal target instead.