Config files can be kept in /etc/webalizer or any other place you wish to 
keep them.  A sample config file is in /etc/webalizer already.

A quick cron can be used to generate all stats for all sites at midnight 
with the folloing code in the root crontab:
0 0 * * * for i in $(find /etc/webalizer -name "*.conf"); do webalizer -c $i &> /dev/null; done