changes in name.conf does not reflect in DNS

[shrestha]

Hello, DNS experts,

We are using NT as a Web server and Linux as a DNS.
We have configured DNS Server and Apache Web server 
in NT. But changes could not be made in Linux Server. 
I have made all changes in name.conf, xx.zone
file and other dependent file, but these changes are
not reflected in DNS configuration window (Bind
Configuration) of Linux. 
 
Name server is also restared after making above
changes in above files.
 
However, if the changes are made in Bind configuration
window, then it update above file as according to the
configuration. 
 
Can someone please tell me how to reflect the changes
that I have made in above files in DNS configuration
window in linux.

Thanks in advance!!! 

Shrestha