Hi YS,
Yes, as you can read in the documentation, using any of the Cfg Actions affects all files that are added after that. So you first need to call the appropriate Cfg Action, then call any of the FileAdd Actions.
As for the protection, if you create a Zip archive and you specify a password, the Zip archive should stay protected, also with subsequent usages. Make sure you use the fixed version of the component I published yesterday, otherwise the password could be reset for files that are added.