As you may know the hacksuite uses files instead of a database to store data. For configuration it's the same thing, this is stored in plain text files. All files that are used to configure the suite can be found in the Data folder, except for vars.php.

There are several ways the suite stores the data, sometimes by adding it to the file as in logs or by overwriting the configuration file eg with adding new tools or ip restrictions.

The majority of configuration files have a structure similar to this:

value|value|value\n
value|value|value\n
value|value|value\n

Files like these always should be parsed by the RawToArray function, which splits the content up and puts it into an array, the example above would produce:

$aData = array();
$aData[0] = array("value","value","value");
$aData[1] = array("value","value","value");
$aData[2] = array("value","value","value");

You can always use the method you prefer to store configuration, I switch between the two methods because I like both.

Not much to tell more about how the configuration works, in a nutshell the suite uses RawToArray to turn configuration files into arrays or includes configuration files when they contain php code.