OK, Brian. I think you'll find
this thread, specifically my response, useful as a way to get things to update on the main volume.
It's always hard to know what you're missing, of course. Basically, you're missing everything that's not shared. We share a few folders in /Library (SyncServices and OpenBase), all of /Users, your OS9 desktop and your 3rd party applications in /Applications. Everything else is copied. (You can see a full list by examining the script -- there's no magic here, and the scripts are completely open.)
So, if something is written outside of the normal "rules" -- that is, in some nonstandard folder, or Users files stored outside their normal locations -- it's on the Sandbox.