MWS config is stored in several XML files located in the MWS database schema as long as they were not extracted to the local config directory of MWS.
Check for MWS/server/default/config folder in your MWS installation directory.
After storing the extracted and modified config back to the database these files can be deleted from the local config directory.
Local config directory has priority before checking the database.
Despite where the concrete config is stored this should survive a restart of the MWS.
Did you check the MWS Administrators Guide, the Monitor Users Guide as well as some BusinessConsole UI documentation for further informations?
If you have some concrete observations and questions, please provide some more details incl. versions, fixes, screenshots etc.