Where to put settings -- 'System' or 'Statement' config file
For most users, simply use the "View settings..." form to specify your conversion settings.
If you were given customized settings, put them in the "system" config (e.g. SC_config_System.txt).
If you have multiple config files...
If you use multiple configuration files (for processing multiple credit card or bank statements) there is no need to re-enter duplicate settings in each the statement configuration file; you may put any common settings in the system config file and those settings will apply every time you use the converter.
Statement config overrides System config
When converting, the system configuration file is read first and then the individual statement configuration file is read. So, if you put the same setting in both files, the value in the statement config file will be the one that is used.