How can I avoid Server Admin overwriting my manual configuration additions?

You can’t. Well actually there are two things you can do to ensure damage is limited.

1. Never modify a configuration file manually while Server Admin is open.
2. Always make sure you have a backup of your configuration files before opening or modifying through Server Admin.

Once you start requiring advanced configuration changes (beyond what Server Admin can do), you will most likely have to give up on Server Admin for Web, Mail and DNS services.

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