Archetype Enhancements for Scrapper can be fitted into any damage power in your primary and secondary. This means it could go into a single target power, or your cones or even the AoE attack Street Justice possesses.
The set is unique, which means even if it is turned Superior with Catalysts, you would not be able to slot another set untouched by Catalysts into your build.
Catalysts can currently only be found from Super Packs and Incarnate Trials, where they're somewhere between rare and purple drops, according to most people. My Stalker has found two so far during Incarnate Trials, in his quest to Incarnate from scratch.
How it's slotted... let's say you stick all six pieces into one power. You would benefit from the entire set bonus the ATE has to offer, in this case:
- Increases maximum health by 1.5%.
- Increases lethal and smashing defense by 2.5% and melee defense by 1.25%.
- Increases damage by 2.5%.
- Improves the Recharge Time of all of your powers by 8.75%.
- Increases Smashing and Lethal resistance by 2.21%.
If you were to Catalyst them all, you would get:
- Increases maximum health by 3%.
- Increases lethal and smashing defense by 5% and melee defense by 2.5%.
- Increases damage by 4%.
- Improves the Recharge Time of all of your powers by 10%.
- Increases Smashing and Lethal resistance by 2.52%.
Now, if you were to use Catalysts to change three of the ATEs into Superior versions, your set bonuses would be from the normal set and the Superior set:
- Increases maximum health by 1.5%.
- Increases lethal and smashing defense by 2.5% and melee defense by 1.25%.
- Increases maximum health by 3%.
- Increases lethal and smashing defense by 5% and melee defense by 2.5%.
On the other side, you may wish to stick three of Scrapper's Strike into one power, and the other three into another power, and then Catalyst all of them so you get the bold part above twice, which could be handy... or you may prefer to keep them all in one power and Catalyst them all for the entire set bonus instead.
Scrapper's Strike: Recharge/Critical Hit Bonus is a special global proc which is activated by any power, not just the power it is slotted in. It increases the chances of criticals a little, but the exact figures I can't remember off the top of my head. Currently, the Superior version doesn't work on live, but a patch to fix that is slated for Issue 22.
Ideon's Paragonwiki page
Member of Paragon/Rogue Knights
Arc: 60092 - Supa Rumble in the Park
"Keep living the dream, and never let any jerk tell you what to do."
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Ideon seems to have answered the question for you plenty well enough, but if you want more info on ATOs or just want to discuss them a bit, you might consider placing your question in the Player Question forum.
Or at least posting it in the scrapper forum with a heading akin to 'ATO Question re:SJ/SR' or something like that.
Thank you @Ideon, that pretty much clarify my question. 
I'm Currently working on a Street Justice/Super Reflex build on my scrapper.... I would appreciate if someone could explain how ATOs work. I plan on maxing out this character lvl and later down the line use it for farming and so on. I want to make this character my best. Any Help would be appreciated.