> Improvements in Ch are automatically changed in your ai file.
Changes to the .ai file made with Illustrator show up in Ch. But changes in Ch do not show up in Illustrator. Ch never changes the artfile files themselves. It just refers to them and keeps all Ch-specific changes in the Ch project.
> Does this mean that all Ch info is stored in the Ai file? Is there an Ch file created Also?
No Ch info is stored in the .ai file. The Ch project (i.e. the Ch Data & Ch Media folders next to the empty .chproj file) stores all changes made in Ch. To see this project, do File > Reveal Project in Finder. Note that you never need to save -- Ch is always saving.
> If I plan the same puppet with many different audio versions, are the versions stored in Ch?
You can reuse a single puppet in multiple scenes (or even in the same scene). All the recordings and scene information are stored in the Ch project. You can drag the puppet from the project panel into an existing scene, or click Add to New Scene to create a new one with the puppet in it. You can also re-import the artwork to create another puppet, for example if you wanted to remove some layers or change keyboard triggers on the 2nd version.
> Could someone on a different system help tweak my puppet in Ai and Ch wand email them back to me without harm?
Yes. For the .ai file you would just replace the new version from your friend in the same location (quit Ch before doing this). Or you can re-point the puppet at the new artwork by selecting the puppet in the project panel and clicking on the blue filepath in the properties panel.
For sharing the Ch project via email it's a little more work: you have to first do File > Copy Media Files into Project Folder and then .zip the project folder (the one that contains the .chproj file, and also your copied media files). Then you can mail the .zip file and your friend can open the .chproj file and it will find the artwork too. When they are finished, they'd do the same zipping steps to send the whole thing back to you.
You could also use dropbox, but the .chproj folder shouldn't be shared that way, only the .zip file (otherwise it could get corrupted if opened by two people at the same time, and also dropbox itself can conflict with Ch when it tries to access the project files).
> Are files inter changeable between Windows/Mac?