It's your call. For the most part we've discouraged doing the triggers in PSD or AI simply because of the lack of flexibility, but it would still work to add (a) (a!) triggers to your original artwork file. We do still recommend doing the + in PSD and AI files because currently you can't make layers independent, but on import CH will convert any +layers into groups to make them work.
A lot depends on the complexity of the puppets - if they're going to take 5 minutes each to rig in CH then I'd just do that, otherwise maybe keeping some of those triggers in the original file might help save some time.
If your puppets are structured EXACTLY the same way, you could do all of your warp independent(+) choices and keyboard triggers in AI or in the Puppet panel. Then when you're done, you could duplicate that puppet in the Project Panel, then re-link it to different AI footage. You can do this in the Properties Panel with the footage selected in the Project Panel.
This will only work if the puppets are structured the exact same way. Once you've linked your different AI files, you could then rig them differently with Sticks and Draggers.
All that said, you're probably best off just rigging them totally separately which is annoying, but far less likely to introduce weird errors.
Thank you! For "EXACTLY" you mean all the names of groups (with trigger keys) or even the untouched levels inside?
Thanks, probably I will duplicate only the mouth sets on Illustrator
I'd recommend updating to the Beta 6 version -- the Duplicate command works better on puppets (does a "deep" duplicate).