Rule selections and customizations are saved in called %APPDATA%\SqlCodeGuard.Addin\settingsv3.xml

The settings file can be input into SQL Code Guard's command line as an input parameter:

eg, when run against a folder of .sql scripts:

sqlcodeguard30.cmd.exe  /source:myscriptsfolder /config:settingsv3.xml /out:results.xml

or against a database instance:

sqlcodeguard30.cmd.exe  /server:myserver\instance /database:mydb /config:settingsv3.xml /out:results.xml