Hey all, first I am SOOO glad I found this as I was going nuts trying to figure this out.. The post from addressler is totally correct, however I just wanted to chime in that if you are using ARC 2 room correction plugin within AU Lab, you should not forget to change your DAW input/output to "Soundflower (2ch)" as well so your mixes are going through the plugin, but bouncing of your audio is not being affected. I am using AU Lab to listen to music, produce music in my DAW and correct my room acoustics so this is important.
Additionally, and perhaps this is an anomaly on my system, but I noticed that I had duplicate (slightly delayed) audio playing causing some phasing issues on playback when using soundflower. I fixed this by leaving all routing the same, but simply quitting Soundflower. I know it sounds crazy, but I quit soundflower and still have my Preferences audio ouput, Au Lab input, and DAW (Logic Pro 9) input AND output set to Soundflower (2 ch) and it works like a charm.
I have AU Lab set to open on startup. Only thing to remember is that when it comes time to track or use your interface to record into the DAW, you must switch the DAW input/output to Saffire (or interface of choice), otherwise your interface is merely your playback device (Soundcard) and does not offer any preamp input options.
Hope this helps someone!