The access control can be done Directory by Directory.
Each Directory has an entry in the httpd.conf file
<Directory>
Order allow,deny
allow from
deny from
</Directory>
See
http://httpd.apache.org/docs-2.0/howto/auth.html for how to use it.
I don't know which configuration tool you are using, but editing the file directly works,
then restart the httpd server.
Regards,
Peter