DNS + Primary Name Server 10.4.11 Server

OK So I have 16 domains on my server. I want access to my server for LDAP + Web and Mail. When setting up domains the server annoyingly puts "NAMESERVER" as the primary DNS server for a domain so it resolves to nameserver.mydomain.com so if i connect via workgroup manager since nameserver is not a proper sub domain it does not work. If I change it to www.mydomain.com as the primary domain then for some reason I can no longer connect to the primary domain.... ??? This is annoying, I used to be able to but not now... What if anything am I doing wrong ??? Thanks...