They hired GM Joel Benjamin and other GMs as a consultant. He studied Kasparov's career for Deep Blue. He could play games against it and help tune it against Kasparov.
I'm willing to bet that they took all of his openings and had Deep Blue put some serious time looking for potential novelties(maybe months) and when they were found, a team of GMs would decide if it was good enough to put into Deep Blue's opening database. They basically nullified Kasparov's repertoire. Studying your opponents games before a match is standard OP. Joel and IBM got to prepare against Kasparov, but he did not get to prepare against Deep Blue.