Apparently, to prepare himself for the cross-dressing scene, Jason Isaacs wandered the drag clubs, picking up on behavior of people there. He wanted to bring Keanu Reeves along, but it would be hard to go undercover with the star of the newly-released The Matrix (1999), so he went alone.
The footage of the radio-controlled submarine under the water was taken from The Hunt for Red October (1990). The first scene of the sub, shows a Soviet Alpha class attack submarine captained by a former student of the Red October's skipper (Sir Sean Connery) and now hunting Red October with orders to destroy it, while the second scene is of the U.S.S. Dallas.
The trivia item below may give away important plot points.
This is the second time Keanu Reeves and Charlize Theron team up to be a couple, the first being The Devil's Advocate (1997), where they are married, doomed, and the next, this movie, as a doomed couple.