After you have set the track I/O the way you want them, go to File/Default Session/Save as Default Session. Then AA will open up each time with those settings.
There are, by the way, a number of other settings that are saved when you click "Save as Default Session." One of these is the track "mono" or "stereo" settings. There is a bar that displays the input selected among the buttons on the left end of the track (it also shows up in the Mixer). Click on the bar, and a menu will pop up giving you the choice of "Stereo" or "Mono" with further selections for which input device channel you want to use. The default is "Stereo," but, again, if you change them to "Mono/[track#]" and save as default, it will always open in that configuration.
Once I figured THAT out, it was easy to assign devices for I/O from the sound cards and MIDI ports and so on...just remember to "Save as Default Session" and you are good to go the next time.
Note that, if you import a session with different settings, 2.0 will conform to its settings when it opens it. I discovered this when I opened up the "Audition Theme." I had set up my I/O to use the ASIO drivers, but when I opened the theme I couldn't hear the playback. It turned out that the theme session used Windows drivers: I had to go back and manually changed to the ASIO for playback...and I had to do this each time I opened the theme up in a new session. When I open an original session, the ASIO drivers are assigned the way I left them.