Superboy Prime is a character that is a Superboy, but he’s not the Superboy that is also Superman. Because comics all need to be consistent and fit in their own little dogmas, comic book creators have developed this complex multiverse where all of the different stories can exist simultaneously without invalidating each other so fanboys can sleep soundly at night. Superboy Prime is from Earth Prime, which is one of many incarnations of the Earth. Earth Prime is from the multiverse before Infinite Crisis.
I believe Ash said that Earth Prime is the “real” Earth, where the readers live. On Earth Prime, people read about Superman and so forth, but apparently there are no superheroes. However, a baby alien from the planet Krypton came to Earth, and he was raised by the Clarks. This boy grew up reading comics, but he didn’t know that he was a Kryptonian and had superpowers. He didn’t know that he was Superboy at first.
In the Crisis on Infinite Earths story, Superman from Earth 1 or Earth 2 jumped the time-space-continuum and got Superboy. DC Comics didn’t want to kill off Superboy, so they had him, Superman from Earth 2, Lois from Earth 2, and Alexander Luthor (not Lex Luthor) all get sucked into a black hole-thingy. After Crisis on Infinite Earths, the creators pretended that Superboy didn’t exist anymore. They didn’t want Superman to have ever been Superboy.
Superboy Prime is the living embodiment of fanboys. He reads comics, but then it turns out that he really is a superhero. However, Superboy Prime eventually turns evil.