Answered a few moments ago, in the thread on changing the TTL.
The templates are in /usr/local/directadmin/templates. Move them to the custom subdirectory, and change them there. Then they'll work for new domains. To make the changes work for old domains, there's a command you send to the DirectAdmin task queue which runs every minute. I'm not taking the time to find it now (it's Sunday and I'm home ) but you can find it on these forums.