Apache configuration has a Directory directive. It is used like a .htaccess file to control access to said directory.

An example:

Order deny,allow
Deny from all
Allow from my.domain.com

The important bit here is the Order statement. Rules will be processed from right to left (in this case all of the deny rules then all of the allow rules. The LAST rule that is matched will the the rule that is used. We are denying everyone and allowing wo we specify.

If you were to specify allow,deny you will be allowing everyone and denying who you specify.

This is quite a complicated system and some personal experimentation should help you understand.