That's why his clone's name is spelled the same way. Captain Atomic didn't actually use the word "clone" as the basis for a clone's name, he just used his own name and put a slight twist in pronouncing it. He didn't tell that Joey though, because he didn't want Joey to know about his secret identity.
At the end of "AP vs Disastro II", Mintenberg asks his army of hang-gliding mice to take home the giant cat mecha that Evil!Bubbles built. We never know what he does with it, but Mintenberg's next major appearance would be "Mintenberg's Armour", in which he's somehow constructed a giant mechanical suit. It's possible that he either used the technology of the cat mecha to help fashion his Powered Armour or he modified the mecha to repurpose it for a human.
How Lacer's A.I. survived the destruction of the shoes is never explained in "Lacer Takes Over". However, in "These Shoes", when Joey goes back to bed after trying on the shoes, Lacer connects itself to Joey's computer to give itself a crash course on Atomic Puppet and learn what else has changed since it was last activated. When Lacer returns, it appears in Joey's computer and pops out in the form of a tiny centipede-shaped microchip. While connected to Joey's computer, Lacer must have taken the opportunity to download and replicate itself in case its original body was destroyed (which it was). Between its appearances, Lacer was probably constructing its new body, which gave it more mobility, the ability to take over other machines, and made it more elusive.
So basically, Manatee-Man was originally a manatee researcher who had a ton of suppressed anger underneath his mellow attitude. On a trip to South America to study the manatees of the Amazonnote , he was attacked by a gang of drug traffickers hiding out in the jungle. The traffickers had been working with poachers to try create some kind of drug from slaughtered manatees (sorta like how Asian medicine often uses the fluids and body parts of rare animals), so they decided to test their first batch on him. Instead, it transformed him into a human-manatee hybrid. Combined with his suppressed anger, which snapped when he learned about the poor manatees that were killed to make the substance, he Hulked Out for the first time. After escaping his captors, he went back to civilization, where he realized he would no longer be able to fit in with his fellow scientists. However, he wasn't interested in being a superhero and he didn't want to turn to a life of crime either, so he decided the best place to use his new form and abilities was in professional wrestling.
Puppet Boy resembles Joey, but has some more similarities with AP: They both have superpowers and a partner they both rely on to power up, and were turned into a puppets out of the blue. We all know Mookie was responsible for turning AP into a puppet, so the version of Mookie (Mookay) from Puppet Boy's universe is a superhero. So if we continue with the Bizarro Universe established, it would be that Puppet Boy was originally Mookay's sidekick in reverse of Captain Atomic and Mookie, but was transformed for some reason (possibly an accident or as a punishment for betrayal).
Roughly halfway through the series, Joey changes his pajamas from a Captain Atomic-themed onesie to a black t-shirt and pants. This change in wardrobe might have been done to subtly indicate Joey had turned 13 somewhere during the season. Combined with the confirmation in "The Big Shift" that the entirety of Season 1 took place over a single year, it is likely Joey celebrated his thirteenth birthday at some point in the series, but we're simply never shown (not to mention, Joey's age is never said in the show, so there's nothing that suggests he remained 12 through the whole season).
- Before series (Mid-February, sometime in early 2010snote ): Captain Atomic is turned into AP by Mookie and teams up with Joey.
- Pilot, Episodes 1-8 (Late February to Early May): The initial adventures of Atomic Puppet, as Joey is introduced to the life of a superhero (like meeting the Justice Alliance and the Rogues Gallery) and AP to civilian life (like Joey getting sick and Pauline learning their secret identity). During this section of episodes, Joey goes to school and wears onesie pajamas.
- Episodes 9-13 (Mid-May through Late June): Joey turns 13 during this period (as possibly evidenced by change of pajamas as mentioned above) and school wraps up shortly after "Erlenmeyer's Revenge". Also, "Something Chicken" features a country fair, something that could take place during the summer.
- Episodes 14-18, except Hero's Holiday (July and August): All these episodes feature no school and 14 and 15 feature summer events, like camping and fishing. More blatantly, Joey outright states "It's the middle of July" in "Snow Maniac".
- Episodes 19-23, as well as Hero's Holiday (September-December): School restarts in these episodes (Warren's mother mentions being late for school, Joey and Pauline in gym class, and a field trip). Being the Christmas Episode, "Hero's Holiday" obviously takes place in December.
- Episodes 24-26 (January and February of the following year): The one year anniversary of Captain Atomic's disappearance and Atomic Puppet's reappearance is celebrated. Also these episodes are placed by the Christmas Episode in some listings, suggesting they take place after it.