How to configure Secure Site to use an htpasswd file for HTTP authentication?

Am I right in thinking that Secure Site is the preferred method of configuring http authentication for Drupal? If so I don't understand how to configure authentication to Drupal using an htpasswd file (and an htgroup file). I already have my htpasswd setup for other websites and users can authenticate against it when I specifically configure Apache accordingly:

AuthType Basic
AuthName "Authorized Zone"
AuthUserFile /srv/conf/htpasswd
Require group authenticated-user

as an example. But how do I use this with Secure Site? I'm completely lost! Thanks