The New Jedi Order series ran from October 1999 to 2003, so the first book came out just a few months after Phantom Menace. Of course this also means that the books were being planned and written several years before, probably in tandem with the Prequel Trilogy production.
So there's a pretty clear delineation in the Star Wars mythos. There's the "Bantam Era" of 1991 to 1999 where books were made with no clue what would occur in the Prequels. Then there's the Del Rey Era (1999 to Present) where they were made in tandem with the Prequels.
This means that there's a lot of things from the Bantam books that were later horribly out of place, books that dealt with clones from the Clone Wars and Luke's mysterious mother and what it meant to be a Jedi. But they've been retroactively fan-wanked into making sense