FWIW, I've just been playing with this.
Steve, you are correct, you can select which track is to contain a synth's automation from the Synth Rack. So, if you wish, you can keep your automation envelopes separate from the MIDI note clips, if you so desire.
I was hoping to be able to create a track for each of the synth parameters that I would ike to automate, but you do not appear to be able to do this, as when you select a new track from the drop down selection thing, what ever automation is contained on the previous track moves onto the newly selected track, and you cannot separate them.
Not to worry, at least I know I can keep the automation envelopes separate from the MIDI clips. I just need to be sure that this gives me some kind of an advantage... it's just a hunch of mine and I will carry on with my experimentation in this area.
@ Jonesey - As far as I can make out, the only automation envelopes that can be created on Audio tracks are those that you would expect to effect an audio clip, and that is Pan and Volume, and also (and I have only just found this out tonight) the various parameters that are tweakable within the ProChannel modules.