You can customize any of the default system packages to change the package or to create a new custom package. When you do so, you can modify the ZENworks Server address and registration key; you cannot modify, add, or remove the ZENworks Agent files.
Only the All Architectures packages are used by the ZENworks Server when completing a deployment task. Therefore, any custom packages you create, or any modifications you make to the x86 or x86_64 system packages, are used only during manual deployments of the ZENworks Agent.