...for some reason, I've noticed I'm one of the few guys running an internally wastegated turbo that's clocked down. It's definitely difficult with the fan right there and the actuator right in front of it almost, but I just consider that much sexier and easier to run way less ic piping :thumbsup
To answer your question though...no you don't have to clock the turbo, it will work facing up like lots of other guys have it done. If it's of any concern to you...my car doesn't have a/c, and is only running one fan.