While this tends to be pretty obvious when the cost is paying Energy, it's less clear if the cost is performing some other effect, like discarding a card or removing Presence.
For instance, Gift of Living Energy (a Minor Power) wouldn't count it towards "If you have at least 2 Sacred Sites...", nor would Fear of the Unseen (a Fear Card) treat it as a Sacred Site for scaring away Invaders.
Note that if you Entwine with River Surges in Sunlight, their River's Domain Special Rule only applies to them (read it as "counts as your Sacred Site"). So for targeting, they would treat any Wetland where either of you have Presence as a Sacred Site, but you would still need 2+ Presence as usual. Tags: Sacred Sites, Presence, Entwined Power, River's Domain (River Surges in Sunlight), 6 more...
What happens to Presence when it gets removed or replaced?
It goes to the destroyed Presence pile in the supply unless the particular effect says to put it elsewhere. From there, it can be restored by any effect that returns destroyed Presence to the island.
As of the release of Nature Incarnate, only four Presence-removing/replacing effects send the Presence somewhere special: "Transform to a Murderous Darkness," "Call Forth Predators" (Sharp Fangs Behind the Leaves special rule), and both Bargains remove replaced Presence from the game. (Though Bargains put the Presence on reminder cards, this is just to help players track how many times they made the Bargain; Bargains scale with the number of times they are made, not the number of Presence on the reminder card. Tags: Replace, Presence, Remove, Bargain, 10 more...
For instance, Downpour Drenches the World could choose its second growth option (which has 2 "Add a Presence" icons), add 1 Presence to uncover a "Move Presence 1" space, use the Move 1 to shift a Presence, then place a second Presence from the new position. Or Many Minds Move as One could gain Energy with its 3rd Growth option, then use it to gain a Power Card before deciding where to place Presence.
Discarding two cards is not listed as a requirement or cost, but as a Growth effect. You must perform that effect to the extent possible. (In this case, you would be left with no cards to play.) Tags: Growth, Downpour Drenches the World, Ember-Eyed Behemoth