You might find it more worth while to move configuration to a file. You can then additionally proceed to create a friendly (web?) interface to modify the values. The script can then write out the new configuration to a file on the server or a file the user can download and upload to the server in their usual manner. Even with documentation someone will ignore/misinterpret the documentation and break things anyway.

Assuming that your average user is smarter than a stick of butter I would go for the type of inline documentation used by Apache and similar programs where they place comments and examples above the actual line, things like;
To enable <feature> uncomment the line below
# BREAD_AND_BUTTER = 1
Having said that, many people struggle with Apache despite it's relatively good documentation