If I use Rhyperior V's "Drill Run" attack against a Darkrai with "Darkness Guard" Ability and only one Darkness Energy card attached, does Darkrai take 20 less damage before discarding the Darkness Energy or is the energy card discarded before the damage is reduced?
If an attack discards energy from the Defending Pokemon, the damage reduction happens first and then apply any attack effects.
Darkness Guard
Source: Darkness Ablaze FAQ (2020-07-31), TPCi Rules Team (2020-08-13)Aug 13, 2020Compendium → Sky Pillar says, "Prevent all effects of the opponent's attacks, including damage, done to Benched Pokemon (both yours and your opponent's)". So does this mean if I use an attack like Zapdos' "Raging Thunder" that I do not apply the bench damage to my own Pokemon?
No, only bench damage done from an opponent's attacks is prevented by Sky Pillar. If your attack does damage to your own Benched Pokemon it is not prevented.
Raging ThunderSky Pillar
Source: TPCi Rules Team (2018-08-09)Aug 9, 2018Compendium →