This is for advanced configurations only. There's a big chance some things won't work as expected so don't play around with this unless you know what you're doing.
The Mailserver is designed to be the best installation for most situations, and sometimes you might want to change a setting, or add some configurations to the Mailserver, which is absolutely fine. There's nothing hidden in the Mailserver configuration.
When doing a major update of the Mailserver, between version 4.3 and 4.4, or 4.4 to 4.5 (when released) expect that some configuration files be overwritten so any local configuration changes are likely to having to be reapplied.
When doing minor updates, only default value changes will overwrite any configuration and update scripts are prepared so that this is done without affecting anything around it.
That said, to be sure, a couple of hook scripts has been provided so that you can ensure that local configuration changes stay the same during updates.
/var/mailserver/config/pre_update_hook.sh
and
/var/mailserver/post_update_hook.sh
In these scripts you can add commands that will run just before and just after the update has taken place.
On top of this, careful documentation of local configuration changes is also key to keeping your system the way you want it through updates.