1) If my understanding of using catalysts is right, ATOs MUST be slotted before they are catalyzed. An ATO sitting in the tray can't be catalyzed.
2) Regular ATOs and Superior ATOs count as different sets for the purpose of set bonuses (and the same set for purposes of slotting), so in your example you do end up with the first 3 bonuses twice, and none of the 4-6 bonuses.
Champion 50s (blueside): Marc Bridge, Nicole Bridge, Fred Blaze, Colleen Storms, Sun's Chariot, Moon's Huntress, Point of Pride
Guardian 50s (redside): Connie Mand
AE arc: Spirit Plane Invasion, #29282, @Honbrid
A couple questions from a returning player regarding catalysts and ATOs:
1) Can you catalyzed ATOs once they have been slotted to a power?
2) If you slot a full ATO set and catalyzed 3 of the 6 pieces, will you get both the (first) 3-part superior bonuses and the (first) 3-part regular bonuses?