If you need to make customized changes to your /etc/httpd/conf/httpd.conf, when custombuild updates apache, your configs will be changed to the new versions of the configs.
Since you're looking for customized versions, you don't want your changes to be lost.
There are 3 ways of making your customizations stick:
the "official" way would be to use the custombuild custom directory method:
mkdir -p custom/ap2
cp -Rp configure/ap2/conf custom/ap2
and then edit your configs in:
as needed. The custom path overrides the default, and won't be overwritten. Your customized files will be used for the overwrite, so you just need to remember to make your changes in the custom path.
If you make changes to the custom files, you can test what result you'll get by typing:
from the custombuild directory.
If you only need to add extra Apache config code to the system, but don't need to remove any existing code, the best way is to add your changes to:
as this file will not be touched by CustomBuild or DirectAdmin. If it doesn't exist, DA will 'touch' it so that it exists, but any changes you add there will be safe from any external changes.
The easiest way would be to run:
chattr +i /etc/httpd/conf/httpd.conf
Then custombuild won't touch it. You can repeat this command on any other files you need, eg /etc/httpd/conf/extra/httpd-alias.conf, etc..
You'd then use:
chattr -i /etc/httpd/conf/httpd.conf
to allow changes again when needed. Don't forget to lock it again after you're done.
Note: For FreeBSD + chattr