The breathing and spaceship sounds came from all speakers. The thing is, I'm not sure if the projectionist had the audio set to some kind of surround emulator similar to what Dolby Pro Logic does in order to get the audio to come out of all speakers but I was sitting right by the rear wall on a balcony level right by some of the surround speakers and heard the breathing coming from there.

Also, when the astronauts attempt to take a picture with the monolith the sound that it emits was deafeningly loud. Everyone in the theater tried to cover their ears after enduring a few seconds of it. It was pretty cool!

Another detail I noticed is that whenever you see the HAL computer he has a greyish hue around him but on the film it was definitely more of a brown than it was grey. Now whether that is due to film color degradation I wouldn't know for sure.