e.g

daemon named -u named -d 3

adding a -d 3 to the startup script results in a named.run being
created in the directory which the script is run from and in
/var/named/

On bootup the named.run is placed in / otherwise in whatever directory
you execute a named start or restart (assuming you deleted all named.run's)

However if you execute an ndc trace named.run is only created in
/var/named.