As for recording straight to Audio Tracks - I don't think that will happen. You will have to bounce the session to disk (individual files). I have read somewhere that there is a program that lets you route Instruments to Audio Tracks so you can record them ....
I think will do what you want with the audio ... otherwise you are gonna have to bounce each individual file to disk, then import to Pro Tools .....
although, Logic Pro does work well with Pro Tools HD ( I think) ..... you may want to consider linking the two ... if you have that option.
As for the Multi thing - it sounds like you are on the right tracks.
If you need more help with that, there are Multi channel Templates on the ToonTrack site. Assuming you are registered user, you can go to
Free Download Section
and get a Multi Template.
Hope this helps!