Ok, so this is kinda weird...
Just now I was literally logging on to the forums to create a post asking about workflow with the TI2; basically the same exact question you're asking.
Great minds think alike, eh.
I am using Logic. When I first got the TI2 I wrongfully assumed that 16 separate slots in the window+ the most advanced virus ever made meant 16 instruments at once.
I was a little let down to see that I couldn't get more than four or five going at a time without note stealing, but that led to my current style of work with the virus, which I actually like quite a bit. Basically what I do now is open up 5 or 6 multi timbral tracks with the TI (just to save space in the project), and keep the ones I'm not using minimized.
Pretty much as soon as I get a sound/sequence/region I like, I'll bounce it and put in the audio file, keep the midi region muted until i need to work with it again, and play around with the audio file. I have found that working with audio files is pretty fun, especially with Logic 9's flex time feature. One I'm working with all audio files, I also don't have to worry about ANY kind of latency or cpu issues and can slap bazillions of effects wherever I want. It is also REALLY nice to be able to use Logic's linear phase EQ with the audio files for the visual aspects of the EQ (even though it pales in comparison to the quality of the virus' EQ)....and BTW if you're a logic user check out the linear phase eq if you haven't....higher quality than the channel EQ but eats up more CPU...great for use with audio files!
So yeah, I basically just press whatever sounds I dig to audio files and work with those. If I need more sounds from the virus, instead of adding more tracks I'll usually just save a preset or two so I can come back to them when I need to, then load in whatever else I need.
I separate my audio file tracks and virus tracks with the ultrabeat track smack dab in the middle (I usually color it yellow or pink just to make it stand out)
All of the virus' midi regions for the entire song will stay under the ultrabeat track, muted, directly under the corresponding audio file so that I can always find them if I need to go back and change something.
Anyway. Sorry if that was a little long- winded, but you stole my idea for the post so I had to lay it all out!
I'm really interested in seeing how other people work with the TI2 as well.