The trailing silence on mixdown has been fixed internally and will be available in the final release. For your second question, do you mean that you have multiple audio devices and you'd like to access both for recording and playback within Audition? While it's not generally recommended for timing-crucial recording, you can create a custom Aggregate Audio Device in OS X's AUDIO MIDI SETUP application, then assign this pseudo-device as your default in Audition.
From /Applications/Utilities/Audio MIDI Setup.app, click the + button to create a new Aggregate Device. Give it a name and select the different inputs and outputs you wish to use. Launch Audition and select this device as your default input/output device from the Preferences > Audio Hardware... menu.
I/O channel names will be difficult to discern as they'll simply be numbered. You can determine the order form the device order in the setup app, or a bit of trial and error may help.
This is probably my lack of knowledge with the software (and mac for that matter). I'll give you my scenario. For my podcast I use soundflower to route a skype output but also want to record my own voice via my USB mic. The USB device is currently my default input on Audtion, and Soundflower also appears in my Audio midi settings. I can't seem to make Audition to pick Soundflower. Just something like recording in Stereo, and recording leg from my Mic and the other from Soundflower, then would mono the mix.
At the moment, I've got to go through the scenario of recording Skype through Audacity and recording my own voice in another software (in this case Audition). I'd love audtion to be my one stop shop!
In Audio MIDI Setup, you'll want to create a new Aggregate Device that includes both your primary audio device and the Soundflower virtual device. Then in Audition, set your audio device to this newly created Aggregate Device. You should then be able to specify inputs and outputs from both devices in Audition.