To support multi-sites (http://drupal.org/getting-started/6/install/multi-site) the module should allow managing a "webalizer.conf" configuation-file per (virtual) host, instead of only a single (default) webalizer.conf file. So, the path of that file should be configurable (per site) and be somewhere within the "sites/{host}/files" directory structure.

Some info on "How to set Webalizer on multiple virtual domain":
http://techgurulive.com/2009/02/11/how-to-install-and-configure-webalize...
http://forums.westhost.com/showthread.php?t=7172