Comparing version numbers is how wyUpdate knows there is a new version. Let's say your customers have version 1.0 and you release a new version "1.1". Half of your users update to version "1.1". Then, you change "1.1" with new files. The users who already updated to "1.1" (before you changed the files) won't see the "new 1.1". Only the users who haven't updated will see the "new 1.1".
So, to answer your questions:
- Yes create separate folders for separate folders.
- Create separate version numbers for changed versions of your app.