>>105865454JSA in All-Star was still the first, but the comics didn't always adhere to continuity so they never really referenced it in the other books as far as I know. But there was a point where National and All-American had some sort of conflicts and All-Star started predominantly using All-American characters and not the National characters, I think.
First official Superman and Batman team-up out of All-Star happened in an issue of Superman, then they turned World's Finest into a Superman/Batman team-up book.
There was the JLA in Brave and the Bold, and then later Brave and the Bold was a team-up book that later became a Batman team-up book.
At some point in the 50's DC acquired the Quality characters but only used Plastic Man and Blackhawk since those were the most popular of Quality's line. Dial H For Hero was the first time they referenced Plastic Man being in Earth-One, I think. I forget when Blackhawk was shown as fully integrated into Earth-One.
"Flash of Two Worlds" was the first time Barry Allen went to Earth-Two and it was made officially where the JSA resided. Subsequent Flash and JLA issues established occasional crossovers between the two worlds.
DC then got the chance to use Captain Marvel and the Marvel Family in the 70's and set them on their own world, on Earth-S. They sometimes had crossovers with Superman and the JLA and the JSA.
Sometime in the 70's Earth-X was introduced and that had the rest of the Quality heroes who weren't Plastic Man or the Blackhawks.
Then Roy Thomas started doing All-Star Squadron and put as many fucking Golden Age heroes from DC and Quality into it, also retconning in the idea that the Quality heroes who were on Earth-X actually came from Earth-Two.
DC got ahold of Charlton in the 1980's and their only appearance as a separate world was in Crisis on Infinite Earths. Then it along with Earth-S and Earth-X and Earth-2 and Earth-1 got merged into one world.