DirectAdmin doesn't manipulate the files in /etc/sysconfig/network-scripts to manage ip#s; it uses it's own files, called ip.list.
The one it uses to start networks at startup is at /usr/local/directadmin/data/admin/ip.list, and contains a list of all the IP#s on the server. The script it uses to add the IP#s is /usr/local/directadmin/scripts/startips.
Writing now specifically about CentOS servers, because that's the distribution I'm most familar with and use on a regular basis, in recent versions of DirectAdmin the scrit is managed with chkconfig, and is copied into /etc/rc.d/init.d (it's called from /etc/rc.d/rc3.d). It's called immediately after the network is setup, at system startup.
Note it's not called with a standard network restart, which is why it needs to bec alled separately if you ever do a network start or restart from the command line in order for the IP#s controlled by DirectAdmin to work.
While it can be run as case stop, (with the K50 prefix), if it is, it does nothing but simply exists without error.
When new IP#s are added or removed in DirectAdmin, they are done so with a direct call to the OS, I believe using ifconfig (if I recall correctly).
Jeff