In an ideal world, the drivers supplied by Apogee would always bypass kMixer. It's a pro unit after all. However, I wouldn't be so sure that's the case in reality. In fact, I would tend to be skeptical. Normal users (the kind who expect to be able to play games and have system sounds mix over on top of that) would lose functionality if kMixer was bypassed in all circumstances.
Apogee probably expects pro users to use ASIO. ASIO will definitely bypass kMixer. Most pro audio software uses ASIO by default.
Unfortunately, I don't know of any way to configure iTunes to use ASIO. Most other playback software does offer this as an option. In particular, you may want to investigate Foobar, which does have an ASIO output plugin.
The other way to determine for sure is to borrow a home theatre receiver from a friend, hook it up to your sound card using a digital connection (coax or optical), and try playing back a DTS/DD PCM-encoded sound file from within iTunes. If you hear music from the home theatre receiver, everything is fine. If you hear static, things are not fine.