In the Superboy comics Pete and Clark are best friends. Pete knows Clark is Superboy but never tells him he does. He helps him much like Lois did on the show. He makes up excuses for Clark's absences.
That was the Silver Age of the comics, though. Everything changed and Superboy doesn't exist in the comics anymore. Clark no longer has a history of Superboy in his life. They did away with Superboy completely from what is now Superman's life story. They decided he existed in I think they called it a pocket universe, or something like that then they destroyed that offshoot universe.
Like with Batman, Superman's friendship with Pete has changed. He and Batman are now rivals and he and Pete are two guys who know each other from school. But then he was killed at one time by the Prankster and Toyman (?) who tortured him until he told them Clark was Superman but he showed up recently as vice-president to Lex Luthor's president of the US.
In some appearances Pete's married to Lana Lang and is jealous of her friendship with Clark- which is close because she knows Clark's secret and Pete doesn't.
I didn't watch Smallville either but I think he did know Clark's secret.
He was never mentioned in TNAOS but he could very well be one of the people who know and help Clark behind the scenes. Jonathan and Martha did wonderfully raising Clark but someone else taught him to be relaxed with people of his own age. Pete, a close cousin, someone was there. The Fortress of Solitude had room for more than one boy.