In most of the cases, there is more than just one website on a server.
Though, it is very important that you can measure the stats of all the websites separately.
I’ll tell you in a few lines how you can achieve this with webalizer.

This tutorial is tested with Webalizer on Ubunty but I presume it will work almost the same way in other distros.

First of all you have to install webalizer on your system.

sudo apt-get install webalizer

After installation of webalizer, the configurationfiles are per default stored in /etc/webalizer.
Move to that directory and make a copy of the config-file.

sudo cp webalizer.conf MySiteName.conf

When the copy is created you have to open it in your favorite editor (I use vim)

sudo vim MySiteName.conf

Scroll down till you find the LogFileattribute and change it to the accesslogfile of MySiteName.
You also have to tell the script where the outputfiles will be stored. This is normally a place which is accessible by the browser.

LogFile /www/mysite/logs/access.log
OutputDir /www/mysite/public_html/webalizer

These are the only 2 parameters which you have to change. You can scroll through the rest of the file and make changes towards your preferences.

All is done now so you can run webalizer with the new configuration file

webalizer -c /etc/webalizer/MySiteName.conf

Webalizer will run and should be accessible through your webbrowser.
Obviously, it would kinda suck if you have to run the webalizerscript every time you want to see the stats so we gonna make a cron which will run the script every hour

crontab -e

And fill in:

0 * * * * webalizer -c /etc/webalizer/MySiteName.conf

Voila, all done