Well heres an attempt at explaining it in the meantime:
MySQL -
MySQL is the central control point of the system. This is where all the sections interact and the first thing you should do is create a MySQL database, and import the .sql file into it.
Web Site:
The website is the main control point. Here you specify what servers you are running. This data is then saved to MySQL.
Perl Daemon:
The perl daemon then uses the info stored in hlstats.conf to connect to MySQL and read the info on servers entered on the website. It will then do various commands to the game server periodically to check it is running.
Game Server:
The game server actually does very little here. All it does is stream logs via UDP to the IP
ort the perl daemon is listening on which simply requires an extra server.cfg command to do (for example: logaddress_add 127.0.0.1:27500).
Contrary to popular belief, the in-game info such as rank, top10, etc,,, and the data shown in the chat window are handled by the perl daemon. It sees something happen in the logs, such as "player A killed Player B with Weapon C" and it will send a command to display that in the chat window via rcon. However this will not show without the HLstatsX addon (use the premium addon, it is fully compatible with HLX:CE).
Hopefully that helps.