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.
If you need to include parameters in httpd.conf or any of your virtual sites’ .conf files (/etc/httpd/sites) that Server Admin cannot digest, you can resort to a little trick:
Create a separate .conf file in a path that Server Admin doesn’t look in and put your parameters in there.
Inside your actual httpd.conf (or virtual site .conf) put a line like the following:
This is not a perfect solution but it will keep conflicts to a minimum.