Say Zoroark GX has Unit Energy {F}{D}{Y} and Rainbow energy attached and uses its "Trickster GX" attack to copy Arceus & Dialga & Palkia GX's "Altered Creation GX" attack. Can Zoroark GX use the extra effect of +1 prize for every KO from Altered Creation GX?
Nope, the two energy attached to Zoroark GX are used to pay for the Trickster GX attack (regardless of how much energy is required for the attack being copied), so in this case there is no "extra Water Energy" to permit the extra +1 prize effect.
Source: TPCi Rules Team (2020-08-13)
Does Channeler negate the effects of Arceus & Dialga & Palkia GX's "Altered Creation GX" attack?
It depends on who is playing the Channeler. If the player who used Altered Creation GX uses Channeler then the effects are removed; the player's Pokemon no longer do +30 damage and the player does not get to take any extra prizes from the effect. However, if the player's opponent plays Channeler, then Altered Creation GX effects are not removed as they reside on the other player (who did not play Channeler).
Source: TPCi Rules Team (2020-01-09)
When I use Arceus & Dialga & Palkia GX's "Altered Creation GX" attack do I take an extra Prize card only if I Knock Out that Active Pokemon with an attack, or do I take an extra Prize for ANY of my opponent's Active Pokemon that get KO'd by my attacks during the rest of the game?
You get to take an extra prize if your Pokemon's attack Knocks Out ANY of your opponent's Active Pokemon during the rest of the game, not just the one that was the Defending Pokemon at the time of the Altered Creation GX attack.
Source: Cosmic Eclipse FAQ (2019-10-18), TPCi Rules Team (2019-10-31)